diff options
Diffstat (limited to 'metadata/md5-cache/sci-biology')
175 files changed, 2157 insertions, 0 deletions
diff --git a/metadata/md5-cache/sci-biology/ApE-2.0.7-r1 b/metadata/md5-cache/sci-biology/ApE-2.0.7-r1 new file mode 100644 index 000000000000..17b2b11a8450 --- /dev/null +++ b/metadata/md5-cache/sci-biology/ApE-2.0.7-r1 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile install +DEPEND=app-arch/unzip +DESCRIPTION=A Plasmid Editor +EAPI=5 +HOMEPAGE=http://www.biology.utah.edu/jorgensen/wayned/ape/ +KEYWORDS=~amd64 ~x86 +LICENSE=ApE +RDEPEND=dev-lang/tcl:0 dev-lang/tk:0 +RESTRICT=bindist mirror +SLOT=0 +SRC_URI=http://www.biology.utah.edu/jorgensen/wayned/ape/Download/Linux/ApE_linux_current.zip -> ApE-2.0.7.zip +_eclasses_=desktop b1d22ac8bdd4679ab79c71aca235009d epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 1d91b03d42ab6308b5f4f6b598ed110e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=ca6aef807b65b2b092f7e1ff4ebbe5e2 diff --git a/metadata/md5-cache/sci-biology/GBrowse-2.48-r1 b/metadata/md5-cache/sci-biology/GBrowse-2.48-r1 new file mode 100644 index 000000000000..b28c160a3d71 --- /dev/null +++ b/metadata/md5-cache/sci-biology/GBrowse-2.48-r1 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile configure install postinst prepare prerm setup test unpack +DEPEND=dev-perl/Module-Build dev-perl/Capture-Tiny !<sci-biology/GBrowse-2.44-r1 >=sci-biology/bioperl-1.6.9 >=dev-perl/Bio-Graphics-2.09 >=dev-perl/GD-2.07 >=dev-perl/CGI-Session-4.02 dev-perl/IO-String dev-perl/JSON dev-perl/libwww-perl dev-perl/Statistics-Descriptive !minimal? ( dev-perl/Bio-Das >=dev-perl/Bio-SamTools-1.20 dev-perl/Crypt-SSLeay dev-perl/DB_File-Lock dev-perl/DBI mysql? ( dev-perl/DBD-mysql ) postgres? ( dev-perl/DBD-Pg ) sqlite? ( dev-perl/DBD-SQLite ) dev-perl/FCGI dev-perl/File-NFSLock dev-perl/GD-SVG dev-perl/Net-OpenID-Consumer dev-perl/Net-SMTP-SSL ) dev-lang/perl:=[-build(-)] >=app-admin/webapp-config-1.50.15 +DESCRIPTION=Generic Model Organism Database Project - The Generic Genome Browser +EAPI=5 +HOMEPAGE=http://gmod.org/wiki/GBrowse +IUSE=-minimal mysql postgres +sqlite vhosts +KEYWORDS=~amd64 ~x86 +LICENSE=|| ( Artistic GPL-1+ ) +RDEPEND=!<sci-biology/GBrowse-2.44-r1 >=sci-biology/bioperl-1.6.9 >=dev-perl/Bio-Graphics-2.09 >=dev-perl/GD-2.07 >=dev-perl/CGI-Session-4.02 dev-perl/IO-String dev-perl/JSON dev-perl/libwww-perl dev-perl/Statistics-Descriptive !minimal? ( dev-perl/Bio-Das >=dev-perl/Bio-SamTools-1.20 dev-perl/Crypt-SSLeay dev-perl/DB_File-Lock dev-perl/DBI mysql? ( dev-perl/DBD-mysql ) postgres? ( dev-perl/DBD-Pg ) sqlite? ( dev-perl/DBD-SQLite ) dev-perl/FCGI dev-perl/File-NFSLock dev-perl/GD-SVG dev-perl/Net-OpenID-Consumer dev-perl/Net-SMTP-SSL ) dev-lang/perl:=[-build(-)] >=app-admin/webapp-config-1.50.15 +SLOT=0 +SRC_URI=mirror://cpan/authors/id/L/LD/LDS/GBrowse-2.48.tar.gz +_eclasses_=desktop b1d22ac8bdd4679ab79c71aca235009d epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 1d91b03d42ab6308b5f4f6b598ed110e multiprocessing cac3169468f893670dac3e7cb940e045 perl-functions 6ec4c4d8fc8324200f1c14e8d158c59b perl-module 97206c028d9bdc9f248e022ac5c9fc83 preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c unpacker 3cd8bad0d31e525cd26be1bfa4e61631 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf webapp 16783e418aca3ffa461d68310bf7ab12 +_md5_=bccaeef3292f6df307fc14fb5a2a74b2 diff --git a/metadata/md5-cache/sci-biology/HTSeq-0.9.1 b/metadata/md5-cache/sci-biology/HTSeq-0.9.1 new file mode 100644 index 000000000000..5bda20184c26 --- /dev/null +++ b/metadata/md5-cache/sci-biology/HTSeq-0.9.1 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile configure install prepare test +DEPEND=dev-python/numpy[python_targets_python3_6(-)?,-python_single_target_python3_6(-)] dev-python/matplotlib[python_targets_python3_6(-)?,-python_single_target_python3_6(-)] sci-biology/pysam[python_targets_python3_6(-)?,-python_single_target_python3_6(-)] >=dev-lang/swig-3.0.8 dev-python/cython[python_targets_python3_6(-)?,-python_single_target_python3_6(-)] python_targets_python3_6? ( dev-lang/python:3.6 ) >=dev-lang/python-exec-2:=[python_targets_python3_6(-)?,-python_single_target_python3_6(-)] dev-python/setuptools[python_targets_python3_6(-)?,-python_single_target_python3_6(-)] +DESCRIPTION=Python support for SAM/BAM/Bowtie/FASTA/Q/GFF/GTF files +EAPI=6 +HOMEPAGE=https://htseq.readthedocs.io/ +IUSE=python_targets_python3_6 +KEYWORDS=~amd64 +LICENSE=GPL-3+ +RDEPEND=dev-python/numpy[python_targets_python3_6(-)?,-python_single_target_python3_6(-)] dev-python/matplotlib[python_targets_python3_6(-)?,-python_single_target_python3_6(-)] sci-biology/pysam[python_targets_python3_6(-)?,-python_single_target_python3_6(-)] python_targets_python3_6? ( dev-lang/python:3.6 ) >=dev-lang/python-exec-2:=[python_targets_python3_6(-)?,-python_single_target_python3_6(-)] +REQUIRED_USE=|| ( python_targets_python3_6 ) +SLOT=0 +SRC_URI=mirror://pypi/H/HTSeq/HTSeq-0.9.1.tar.gz +_eclasses_=desktop b1d22ac8bdd4679ab79c71aca235009d distutils-r1 c576838cd67e384002a18edd54be710e epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 ltprune 2729691420b6deeda2a90b1f1183fb55 multibuild 40fe59465edacd730c644ec2bc197809 multilib 1d91b03d42ab6308b5f4f6b598ed110e multiprocessing cac3169468f893670dac3e7cb940e045 preserve-libs ef207dc62baddfddfd39a164d9797648 python-r1 4eed5e0c72d4544a2291ae46515f5d79 python-utils-r1 611c493a4cfef5254350fabc04b606f5 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf xdg-utils ff2ff954e6b17929574eee4efc5152ba +_md5_=1a7e20f6705425c8dc29ce2c240db0b2 diff --git a/metadata/md5-cache/sci-biology/HTSeq-9999 b/metadata/md5-cache/sci-biology/HTSeq-9999 new file mode 100644 index 000000000000..17c9c8faa44e --- /dev/null +++ b/metadata/md5-cache/sci-biology/HTSeq-9999 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile configure install prepare test unpack +DEPEND=dev-python/numpy[python_targets_python3_6(-)?,-python_single_target_python3_6(-)] dev-python/matplotlib[python_targets_python3_6(-)?,-python_single_target_python3_6(-)] sci-biology/pysam[python_targets_python3_6(-)?,-python_single_target_python3_6(-)] >=dev-lang/swig-3.0.8 dev-python/cython[python_targets_python3_6(-)?,-python_single_target_python3_6(-)] python_targets_python3_6? ( dev-lang/python:3.6 ) >=dev-lang/python-exec-2:=[python_targets_python3_6(-)?,-python_single_target_python3_6(-)] dev-python/setuptools[python_targets_python3_6(-)?,-python_single_target_python3_6(-)] >=dev-vcs/git-1.8.2.1[curl] +DESCRIPTION=Python support for SAM/BAM/Bowtie/FASTA/Q/GFF/GTF files +EAPI=6 +HOMEPAGE=https://htseq.readthedocs.io/ +IUSE=python_targets_python3_6 +LICENSE=GPL-3+ +PROPERTIES=live +RDEPEND=dev-python/numpy[python_targets_python3_6(-)?,-python_single_target_python3_6(-)] dev-python/matplotlib[python_targets_python3_6(-)?,-python_single_target_python3_6(-)] sci-biology/pysam[python_targets_python3_6(-)?,-python_single_target_python3_6(-)] python_targets_python3_6? ( dev-lang/python:3.6 ) >=dev-lang/python-exec-2:=[python_targets_python3_6(-)?,-python_single_target_python3_6(-)] +REQUIRED_USE=|| ( python_targets_python3_6 ) +SLOT=0 +_eclasses_=desktop b1d22ac8bdd4679ab79c71aca235009d distutils-r1 c576838cd67e384002a18edd54be710e epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 git-r3 809e27702c573cbba31c08ed00bbad33 ltprune 2729691420b6deeda2a90b1f1183fb55 multibuild 40fe59465edacd730c644ec2bc197809 multilib 1d91b03d42ab6308b5f4f6b598ed110e multiprocessing cac3169468f893670dac3e7cb940e045 preserve-libs ef207dc62baddfddfd39a164d9797648 python-r1 4eed5e0c72d4544a2291ae46515f5d79 python-utils-r1 611c493a4cfef5254350fabc04b606f5 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf xdg-utils ff2ff954e6b17929574eee4efc5152ba +_md5_=1a7e20f6705425c8dc29ce2c240db0b2 diff --git a/metadata/md5-cache/sci-biology/STAR-2.5.3a b/metadata/md5-cache/sci-biology/STAR-2.5.3a new file mode 100644 index 000000000000..ea68d9b21e81 --- /dev/null +++ b/metadata/md5-cache/sci-biology/STAR-2.5.3a @@ -0,0 +1,12 @@ +DEFINED_PHASES=compile configure install pretend setup +DEPEND=sci-libs/htslib:= virtual/pkgconfig +DESCRIPTION=STAR aligner: align RNA-seq reads to reference genome uncompressed suffix arrays +EAPI=6 +HOMEPAGE=https://github.com/alexdobin/STAR +KEYWORDS=~amd64 +LICENSE=GPL-3 +RDEPEND=sci-libs/htslib:= +SLOT=0 +SRC_URI=https://github.com/alexdobin/STAR/archive/2.5.3a.tar.gz -> STAR-2.5.3a.tar.gz +_eclasses_=multilib 1d91b03d42ab6308b5f4f6b598ed110e toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c +_md5_=1eb821b9192887ab1f2ac6b1536037ac diff --git a/metadata/md5-cache/sci-biology/aaindex-9.1-r1 b/metadata/md5-cache/sci-biology/aaindex-9.1-r1 new file mode 100644 index 000000000000..618805eb016b --- /dev/null +++ b/metadata/md5-cache/sci-biology/aaindex-9.1-r1 @@ -0,0 +1,12 @@ +DEFINED_PHASES=compile install +DEPEND=emboss? ( sci-biology/emboss ) +DESCRIPTION=Amino acid indices and similarity matrices +EAPI=6 +HOMEPAGE=https://www.genome.jp/aaindex/ +IUSE=emboss minimal +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux +LICENSE=public-domain +RDEPEND=emboss? ( sci-biology/emboss ) +SLOT=0 +SRC_URI=mirror://gentoo/aaindex-9.1.tar.bz2 +_md5_=8636229aaffdb1c6d95611b06d3cd161 diff --git a/metadata/md5-cache/sci-biology/abyss-2.0.2-r1 b/metadata/md5-cache/sci-biology/abyss-2.0.2-r1 new file mode 100644 index 000000000000..fb3872cb835e --- /dev/null +++ b/metadata/md5-cache/sci-biology/abyss-2.0.2-r1 @@ -0,0 +1,13 @@ +DEFINED_PHASES=configure prepare pretend setup +DEPEND=dev-cpp/sparsehash dev-libs/boost:= misc-haskell? ( dev-libs/gmp:0= virtual/libffi:0= ) mpi? ( sys-cluster/openmpi ) misc-haskell? ( dev-lang/ghc dev-haskell/mmap ) >=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 +DESCRIPTION=Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler +EAPI=6 +HOMEPAGE=http://www.bcgsc.ca/platform/bioinfo/software/abyss/ +IUSE=+mpi openmp misc-haskell +KEYWORDS=~amd64 ~x86 +LICENSE=abyss +RDEPEND=dev-cpp/sparsehash dev-libs/boost:= misc-haskell? ( dev-libs/gmp:0= virtual/libffi:0= ) mpi? ( sys-cluster/openmpi ) +SLOT=0 +SRC_URI=https://github.com/bcgsc/abyss/archive/2.0.2.tar.gz -> abyss-2.0.2.tar.gz +_eclasses_=autotools ea7865c8fba1ea8d3639f355fffe1a3c libtool f143db5a74ccd9ca28c1234deffede96 multilib 1d91b03d42ab6308b5f4f6b598ed110e toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c +_md5_=3b173739bd4e2f9d61a49918b3b8bc05 diff --git a/metadata/md5-cache/sci-biology/abyss-2.0.3 b/metadata/md5-cache/sci-biology/abyss-2.0.3 new file mode 100644 index 000000000000..8684b913588b --- /dev/null +++ b/metadata/md5-cache/sci-biology/abyss-2.0.3 @@ -0,0 +1,13 @@ +DEFINED_PHASES=configure prepare pretend setup +DEPEND=dev-cpp/sparsehash dev-libs/boost:= misc-haskell? ( dev-libs/gmp:0= virtual/libffi:0= ) mpi? ( sys-cluster/openmpi ) misc-haskell? ( dev-lang/ghc ) >=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 +DESCRIPTION=Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler +EAPI=6 +HOMEPAGE=http://www.bcgsc.ca/platform/bioinfo/software/abyss/ +IUSE=+mpi openmp misc-haskell +KEYWORDS=~amd64 ~x86 +LICENSE=abyss +RDEPEND=dev-cpp/sparsehash dev-libs/boost:= misc-haskell? ( dev-libs/gmp:0= virtual/libffi:0= ) mpi? ( sys-cluster/openmpi ) +SLOT=0 +SRC_URI=https://github.com/bcgsc/abyss/archive/2.0.3.tar.gz -> abyss-2.0.3.tar.gz +_eclasses_=autotools ea7865c8fba1ea8d3639f355fffe1a3c libtool f143db5a74ccd9ca28c1234deffede96 multilib 1d91b03d42ab6308b5f4f6b598ed110e toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c +_md5_=4c70cbdf60d5dc2d564272b103f2b469 diff --git a/metadata/md5-cache/sci-biology/amap-2.2-r3 b/metadata/md5-cache/sci-biology/amap-2.2-r3 new file mode 100644 index 000000000000..89ab50a4d475 --- /dev/null +++ b/metadata/md5-cache/sci-biology/amap-2.2-r3 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile configure install preinst prepare setup +DEPEND=java? ( >=virtual/jdk-1.5 ) java? ( >=dev-java/java-config-2.2.0-r3 ) java? ( >=dev-java/ant-core-1.8.2:0 >=dev-java/javatoolkit-0.3.0-r2 ) +DESCRIPTION=Protein multiple-alignment-based sequence annealing +EAPI=6 +HOMEPAGE=http://bio.math.berkeley.edu/amap/ +IUSE=java elibc_FreeBSD java elibc_FreeBSD +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-2 +RDEPEND=java? ( >=virtual/jre-1.5 ) java? ( >=dev-java/java-config-2.2.0-r3 ) +SLOT=0 +SRC_URI=http://baboon.math.berkeley.edu/amap/download/amap.2.2.tar.gz +_eclasses_=desktop b1d22ac8bdd4679ab79c71aca235009d eapi7-ver 756b3f27d8e46131d5cf3c51bd876446 epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 java-ant-2 8d9cb415f1ca9fc7ebc5a74bacec300c java-pkg-opt-2 77d2e22d0de7640f817d20e861c0ff3f java-utils-2 a055407af6fd37cf3f692ba73d2d2ba5 ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 1d91b03d42ab6308b5f4f6b598ed110e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf versionator 2352c3fc97241f6a02042773c8287748 +_md5_=6bd792e8b76c06ee993b88f83e48b907 diff --git a/metadata/md5-cache/sci-biology/amos-3.1.0-r4 b/metadata/md5-cache/sci-biology/amos-3.1.0-r4 new file mode 100644 index 000000000000..cdc1848c8e15 --- /dev/null +++ b/metadata/md5-cache/sci-biology/amos-3.1.0-r4 @@ -0,0 +1,14 @@ +DEFINED_PHASES=configure install prepare setup +DEPEND=>=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 +DESCRIPTION=A Modular, Open-Source whole genome assembler +EAPI=6 +HOMEPAGE=http://amos.sourceforge.net/ +IUSE=+python_targets_python2_7 +python_single_target_python2_7 +KEYWORDS=~amd64 ~x86 +LICENSE=Artistic +RDEPEND=python_single_target_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 >=dev-lang/python-exec-2:=[python_targets_python2_7] ) dev-perl/DBI dev-perl/Statistics-Descriptive sci-biology/mummer +REQUIRED_USE=^^ ( python_single_target_python2_7 ) python_single_target_python2_7? ( python_targets_python2_7 ) +SLOT=0 +SRC_URI=mirror://sourceforge/amos/amos-3.1.0.tar.gz https://dev.gentoo.org/~soap/distfiles/amos-3.1.0-fix-c++14.patch.bz2 +_eclasses_=autotools ea7865c8fba1ea8d3639f355fffe1a3c desktop b1d22ac8bdd4679ab79c71aca235009d epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 flag-o-matic dc34234e8c43343da45853da22dcf14b libtool f143db5a74ccd9ca28c1234deffede96 ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 1d91b03d42ab6308b5f4f6b598ed110e preserve-libs ef207dc62baddfddfd39a164d9797648 python-single-r1 36ac48e647d2627de28c87aaffb94753 python-utils-r1 611c493a4cfef5254350fabc04b606f5 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=aec6d1c76d5ea621c66e803800e2b3c4 diff --git a/metadata/md5-cache/sci-biology/augustus-2.5.5 b/metadata/md5-cache/sci-biology/augustus-2.5.5 new file mode 100644 index 000000000000..8b5104561aff --- /dev/null +++ b/metadata/md5-cache/sci-biology/augustus-2.5.5 @@ -0,0 +1,11 @@ +DEFINED_PHASES=compile configure install +DESCRIPTION=Eukaryotic gene predictor +EAPI=7 +HOMEPAGE=http://augustus.gobics.de/ +IUSE=examples +KEYWORDS=amd64 x86 +LICENSE=Artistic +SLOT=0 +SRC_URI=http://augustus.gobics.de/binaries/augustus.2.5.5.tar.gz +_eclasses_=multilib 1d91b03d42ab6308b5f4f6b598ed110e toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c +_md5_=80962b244c7531e320f35904727b5bd5 diff --git a/metadata/md5-cache/sci-biology/bamtools-2.5.1 b/metadata/md5-cache/sci-biology/bamtools-2.5.1 new file mode 100644 index 000000000000..100a6ae2ac92 --- /dev/null +++ b/metadata/md5-cache/sci-biology/bamtools-2.5.1 @@ -0,0 +1,13 @@ +BDEPEND=virtual/pkgconfig dev-util/ninja dev-util/cmake +DEFINED_PHASES=compile configure install prepare test +DEPEND=>=dev-libs/jsoncpp-1.8.0:= sys-libs/zlib:= +DESCRIPTION=A programmer's API and an end-user's toolkit for handling BAM files +EAPI=7 +HOMEPAGE=https://github.com/pezmaster31/bamtools +KEYWORDS=~amd64 ~x86 +LICENSE=MIT +RDEPEND=>=dev-libs/jsoncpp-1.8.0:= sys-libs/zlib:= +SLOT=0/2.5.1 +SRC_URI=https://github.com/pezmaster31/bamtools/archive/v2.5.1.tar.gz -> bamtools-2.5.1.tar.gz +_eclasses_=cmake 7b250250bd1c3cc90800ed668fb87825 eutils fcb2aa98e1948b835b5ae66ca52868c5 flag-o-matic dc34234e8c43343da45853da22dcf14b multilib 1d91b03d42ab6308b5f4f6b598ed110e multiprocessing cac3169468f893670dac3e7cb940e045 ninja-utils 132cbb376048d079b5a012f5467c4e7f toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c xdg-utils ff2ff954e6b17929574eee4efc5152ba +_md5_=a2299dc6ca850c1c25582656d7586681 diff --git a/metadata/md5-cache/sci-biology/bamtools-9999 b/metadata/md5-cache/sci-biology/bamtools-9999 new file mode 100644 index 000000000000..0ded7aaedb19 --- /dev/null +++ b/metadata/md5-cache/sci-biology/bamtools-9999 @@ -0,0 +1,12 @@ +BDEPEND=virtual/pkgconfig dev-util/ninja dev-util/cmake >=dev-vcs/git-1.8.2.1[curl] +DEFINED_PHASES=compile configure install prepare test unpack +DEPEND=>=dev-libs/jsoncpp-1.8.0:= sys-libs/zlib:= +DESCRIPTION=A programmer's API and an end-user's toolkit for handling BAM files +EAPI=7 +HOMEPAGE=https://github.com/pezmaster31/bamtools +LICENSE=MIT +PROPERTIES=live +RDEPEND=>=dev-libs/jsoncpp-1.8.0:= sys-libs/zlib:= +SLOT=0/9999 +_eclasses_=cmake 7b250250bd1c3cc90800ed668fb87825 eutils fcb2aa98e1948b835b5ae66ca52868c5 flag-o-matic dc34234e8c43343da45853da22dcf14b git-r3 809e27702c573cbba31c08ed00bbad33 multilib 1d91b03d42ab6308b5f4f6b598ed110e multiprocessing cac3169468f893670dac3e7cb940e045 ninja-utils 132cbb376048d079b5a012f5467c4e7f toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c xdg-utils ff2ff954e6b17929574eee4efc5152ba +_md5_=a2299dc6ca850c1c25582656d7586681 diff --git a/metadata/md5-cache/sci-biology/bcftools-1.5 b/metadata/md5-cache/sci-biology/bcftools-1.5 new file mode 100644 index 000000000000..2d0cca393435 --- /dev/null +++ b/metadata/md5-cache/sci-biology/bcftools-1.5 @@ -0,0 +1,14 @@ +DEFINED_PHASES=configure prepare +DEPEND=dev-lang/perl =sci-libs/htslib-1.5*:= sys-libs/zlib python_targets_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 ) >=dev-lang/python-exec-2:=[python_targets_python2_7(-)?,-python_single_target_python2_7(-)] +DESCRIPTION=Utilities for variant calling and manipulating VCF and BCF files +EAPI=6 +HOMEPAGE=http://www.htslib.org +IUSE=python_targets_python2_7 +KEYWORDS=~amd64 ~x86 +LICENSE=MIT +RDEPEND=dev-lang/perl =sci-libs/htslib-1.5*:= sys-libs/zlib python_targets_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 ) >=dev-lang/python-exec-2:=[python_targets_python2_7(-)?,-python_single_target_python2_7(-)] +REQUIRED_USE=|| ( python_targets_python2_7 ) +SLOT=0 +SRC_URI=https://github.com/samtools/bcftools/releases/download/1.5/bcftools-1.5.tar.bz2 +_eclasses_=multibuild 40fe59465edacd730c644ec2bc197809 multilib 1d91b03d42ab6308b5f4f6b598ed110e python-r1 4eed5e0c72d4544a2291ae46515f5d79 python-utils-r1 611c493a4cfef5254350fabc04b606f5 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c +_md5_=e289371e3fec376baf8fe36c652ca521 diff --git a/metadata/md5-cache/sci-biology/bcftools-1.9-r1 b/metadata/md5-cache/sci-biology/bcftools-1.9-r1 new file mode 100644 index 000000000000..adf554cc9a20 --- /dev/null +++ b/metadata/md5-cache/sci-biology/bcftools-1.9-r1 @@ -0,0 +1,14 @@ +DEFINED_PHASES=configure prepare setup +DEPEND=dev-lang/perl dev-python/matplotlib[python_targets_python3_6(-)?,-python_single_target_pypy3(-),-python_single_target_python2_7(-),-python_single_target_python3_7(-),-python_single_target_python3_8(-),python_single_target_python3_6(+)?] =sci-libs/htslib-1.9*:= sys-libs/zlib:= python_single_target_python3_6? ( dev-lang/python:3.6 >=dev-lang/python-exec-2:=[python_targets_python3_6] ) +DESCRIPTION=Utilities for variant calling and manipulating VCF and BCF files +EAPI=7 +HOMEPAGE=http://www.htslib.org +IUSE=+python_targets_python3_6 +python_single_target_python3_6 +KEYWORDS=~amd64 ~x86 +LICENSE=MIT +RDEPEND=dev-lang/perl dev-python/matplotlib[python_targets_python3_6(-)?,-python_single_target_pypy3(-),-python_single_target_python2_7(-),-python_single_target_python3_7(-),-python_single_target_python3_8(-),python_single_target_python3_6(+)?] =sci-libs/htslib-1.9*:= sys-libs/zlib:= python_single_target_python3_6? ( dev-lang/python:3.6 >=dev-lang/python-exec-2:=[python_targets_python3_6] ) +REQUIRED_USE=^^ ( python_single_target_python3_6 ) python_single_target_python3_6? ( python_targets_python3_6 ) +SLOT=0 +SRC_URI=https://github.com/samtools/bcftools/releases/download/1.9/bcftools-1.9.tar.bz2 +_eclasses_=multilib 1d91b03d42ab6308b5f4f6b598ed110e python-single-r1 36ac48e647d2627de28c87aaffb94753 python-utils-r1 611c493a4cfef5254350fabc04b606f5 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c +_md5_=ab648b9a40f6f3d4b54a7f2b872dbfca diff --git a/metadata/md5-cache/sci-biology/bedtools-2.26.0 b/metadata/md5-cache/sci-biology/bedtools-2.26.0 new file mode 100644 index 000000000000..a391db0844e9 --- /dev/null +++ b/metadata/md5-cache/sci-biology/bedtools-2.26.0 @@ -0,0 +1,14 @@ +DEFINED_PHASES=configure install setup +DEPEND=|| ( dev-lang/python:3.6 >=dev-lang/python-2.7.5-r2:2.7 ) test? ( sci-libs/htslib sci-biology/samtools:0 ) +DESCRIPTION=Tools for manipulation and analysis of BED, GFF/GTF, VCF, SAM/BAM file formats +EAPI=6 +HOMEPAGE=https://bedtools.readthedocs.io/ +IUSE=test +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-2 +RDEPEND=sys-libs/zlib +RESTRICT=!test? ( test ) +SLOT=0 +SRC_URI=https://github.com/arq5x/bedtools2/releases/download/v2.26.0/bedtools-2.26.0.tar.gz https://dev.gentoo.org/~mgorny/dist/bedtools-2.26.0-fix-buildsystem.patch.bz2 +_eclasses_=desktop b1d22ac8bdd4679ab79c71aca235009d epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 flag-o-matic dc34234e8c43343da45853da22dcf14b ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 1d91b03d42ab6308b5f4f6b598ed110e preserve-libs ef207dc62baddfddfd39a164d9797648 python-any-r1 b6db354660033efd06cd6d7f4905ccea python-utils-r1 611c493a4cfef5254350fabc04b606f5 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=7823f0eb8a9e0d9782d2caf65208df9e diff --git a/metadata/md5-cache/sci-biology/bfast-0.7.0a b/metadata/md5-cache/sci-biology/bfast-0.7.0a new file mode 100644 index 000000000000..19eedacaf754 --- /dev/null +++ b/metadata/md5-cache/sci-biology/bfast-0.7.0a @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile configure install prepare test +DEPEND=>=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 +DESCRIPTION=Blat-like Fast Accurate Search Tool +EAPI=5 +HOMEPAGE=https://sourceforge.net/projects/bfast/ +IUSE=test +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-2 +RDEPEND=dev-perl/XML-Simple +RESTRICT=!test? ( test ) +SLOT=0 +SRC_URI=mirror://sourceforge/bfast/bfast-0.7.0a.tar.gz +_eclasses_=autotools ea7865c8fba1ea8d3639f355fffe1a3c autotools-utils 95db0904ad0f62535e18e5ccb67cce5e desktop b1d22ac8bdd4679ab79c71aca235009d epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 flag-o-matic dc34234e8c43343da45853da22dcf14b libtool f143db5a74ccd9ca28c1234deffede96 ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 1d91b03d42ab6308b5f4f6b598ed110e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=f752137cf374be5cbb2754f3aa98ad0d diff --git a/metadata/md5-cache/sci-biology/biogrep-1.0-r2 b/metadata/md5-cache/sci-biology/biogrep-1.0-r2 new file mode 100644 index 000000000000..b0a54af87a0e --- /dev/null +++ b/metadata/md5-cache/sci-biology/biogrep-1.0-r2 @@ -0,0 +1,12 @@ +DEFINED_PHASES=install prepare +DEPEND=>=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 +DESCRIPTION=Multithreaded tool for matching large sets of patterns against biosequence DBs +EAPI=6 +HOMEPAGE=http://stephanopoulos.openwetware.org/BIOGREP.html +IUSE=doc examples +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-2 +SLOT=0 +SRC_URI=http://www.openwetware.org/images/3/3d/Biogrep-1.0.tar.gz -> biogrep-1.0.tar.gz doc? ( http://www.openwetware.org/images/4/49/Biogrep.pdf -> biogrep-1.0.pdf ) +_eclasses_=autotools ea7865c8fba1ea8d3639f355fffe1a3c libtool f143db5a74ccd9ca28c1234deffede96 multilib 1d91b03d42ab6308b5f4f6b598ed110e toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c +_md5_=9731727dae2a2514bcaa486b0059272e diff --git a/metadata/md5-cache/sci-biology/biopandas-0.2.1 b/metadata/md5-cache/sci-biology/biopandas-0.2.1 new file mode 100644 index 000000000000..389c4f8456bf --- /dev/null +++ b/metadata/md5-cache/sci-biology/biopandas-0.2.1 @@ -0,0 +1,15 @@ +DEFINED_PHASES=compile configure install prepare test +DEPEND=dev-python/numpy[python_targets_python3_6(-)?,-python_single_target_python3_6(-)] dev-python/pandas[python_targets_python3_6(-)?,-python_single_target_python3_6(-)] sci-libs/scipy[python_targets_python3_6(-)?,-python_single_target_python3_6(-)] dev-python/setuptools[python_targets_python3_6(-)?,-python_single_target_python3_6(-)] test? ( dev-python/nose[python_targets_python3_6(-)?,-python_single_target_python3_6(-)] ) python_targets_python3_6? ( dev-lang/python:3.6 ) >=dev-lang/python-exec-2:=[python_targets_python3_6(-)?,-python_single_target_python3_6(-)] dev-python/setuptools[python_targets_python3_6(-)?,-python_single_target_python3_6(-)] +DESCRIPTION=Molecular Structures in Pandas DataFrames +EAPI=6 +HOMEPAGE=https://rasbt.github.io/biopandas/ https://github.com/rasbt/biopandas https://pypi.org/project/BioPandas/ +IUSE=test python_targets_python3_6 +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux +LICENSE=BSD +RDEPEND=dev-python/numpy[python_targets_python3_6(-)?,-python_single_target_python3_6(-)] dev-python/pandas[python_targets_python3_6(-)?,-python_single_target_python3_6(-)] sci-libs/scipy[python_targets_python3_6(-)?,-python_single_target_python3_6(-)] python_targets_python3_6? ( dev-lang/python:3.6 ) >=dev-lang/python-exec-2:=[python_targets_python3_6(-)?,-python_single_target_python3_6(-)] +REQUIRED_USE=|| ( python_targets_python3_6 ) +RESTRICT=!test? ( test ) +SLOT=0 +SRC_URI=mirror://pypi/B/BioPandas/biopandas-0.2.1.tar.gz +_eclasses_=desktop b1d22ac8bdd4679ab79c71aca235009d distutils-r1 c576838cd67e384002a18edd54be710e epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 ltprune 2729691420b6deeda2a90b1f1183fb55 multibuild 40fe59465edacd730c644ec2bc197809 multilib 1d91b03d42ab6308b5f4f6b598ed110e multiprocessing cac3169468f893670dac3e7cb940e045 preserve-libs ef207dc62baddfddfd39a164d9797648 python-r1 4eed5e0c72d4544a2291ae46515f5d79 python-utils-r1 611c493a4cfef5254350fabc04b606f5 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf xdg-utils ff2ff954e6b17929574eee4efc5152ba +_md5_=9aa50282a8f020366a788665165393c5 diff --git a/metadata/md5-cache/sci-biology/bioperl-1.6.9 b/metadata/md5-cache/sci-biology/bioperl-1.6.9 new file mode 100644 index 000000000000..fc13a84f7d08 --- /dev/null +++ b/metadata/md5-cache/sci-biology/bioperl-1.6.9 @@ -0,0 +1,15 @@ +DEFINED_PHASES=compile configure install prepare test unpack +DEPEND=dev-perl/Module-Build dev-perl/libwww-perl !minimal? ( dev-perl/Algorithm-Munkres dev-perl/Array-Compare dev-perl/YAML dev-perl/Bio-ASN1-EntrezGene dev-perl/Clone dev-perl/Convert-Binary-C dev-perl/Data-Stag dev-perl/GD dev-perl/Graph >=dev-perl/HTML-Parser-3.60 dev-perl/List-MoreUtils dev-perl/Math-Random dev-perl/PostScript dev-perl/Set-Scalar dev-perl/SOAP-Lite dev-perl/Sort-Naturally dev-perl/Spreadsheet-ParseExcel >=virtual/perl-Storable-2.05 >=dev-perl/SVG-2.26 >=dev-perl/SVG-Graph-0.01 dev-perl/URI >=dev-perl/XML-DOM-XPath-0.13 dev-perl/XML-Parser >=dev-perl/XML-SAX-0.15 dev-perl/XML-Simple dev-perl/XML-Twig >=dev-perl/XML-Writer-0.4 dev-perl/XML-DOM dev-perl/XML-XPath ) graphviz? ( dev-perl/GraphViz ) sqlite? ( dev-perl/DBD-SQLite ) dev-lang/perl:=[-build(-)] +DESCRIPTION=Perl tools for bioinformatics - Core modules +EAPI=5 +HOMEPAGE=http://www.bioperl.org/ +IUSE=-minimal graphviz sqlite +db +network +run +KEYWORDS=amd64 x86 +LICENSE=|| ( Artistic GPL-1+ ) +PDEPEND=db? ( >=sci-biology/bioperl-db-1.6.9 ) network? ( >=sci-biology/bioperl-network-1.6.9 ) run? ( >=sci-biology/bioperl-run-1.6.9 ) +RDEPEND=dev-perl/libwww-perl !minimal? ( dev-perl/Algorithm-Munkres dev-perl/Array-Compare dev-perl/YAML dev-perl/Bio-ASN1-EntrezGene dev-perl/Clone dev-perl/Convert-Binary-C dev-perl/Data-Stag dev-perl/GD dev-perl/Graph >=dev-perl/HTML-Parser-3.60 dev-perl/List-MoreUtils dev-perl/Math-Random dev-perl/PostScript dev-perl/Set-Scalar dev-perl/SOAP-Lite dev-perl/Sort-Naturally dev-perl/Spreadsheet-ParseExcel >=virtual/perl-Storable-2.05 >=dev-perl/SVG-2.26 >=dev-perl/SVG-Graph-0.01 dev-perl/URI >=dev-perl/XML-DOM-XPath-0.13 dev-perl/XML-Parser >=dev-perl/XML-SAX-0.15 dev-perl/XML-Simple dev-perl/XML-Twig >=dev-perl/XML-Writer-0.4 dev-perl/XML-DOM dev-perl/XML-XPath ) graphviz? ( dev-perl/GraphViz ) sqlite? ( dev-perl/DBD-SQLite ) dev-lang/perl:=[-build(-)] +REQUIRED_USE=minimal? ( !graphviz ) +SLOT=0 +SRC_URI=mirror://cpan/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.901.tar.gz +_eclasses_=desktop b1d22ac8bdd4679ab79c71aca235009d epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 1d91b03d42ab6308b5f4f6b598ed110e multiprocessing cac3169468f893670dac3e7cb940e045 perl-functions 6ec4c4d8fc8324200f1c14e8d158c59b perl-module 97206c028d9bdc9f248e022ac5c9fc83 preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c unpacker 3cd8bad0d31e525cd26be1bfa4e61631 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=be22a76392a6e5c121e4b6d388045faa diff --git a/metadata/md5-cache/sci-biology/bioperl-db-1.6.9 b/metadata/md5-cache/sci-biology/bioperl-db-1.6.9 new file mode 100644 index 000000000000..762791d6760e --- /dev/null +++ b/metadata/md5-cache/sci-biology/bioperl-db-1.6.9 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile configure install prepare test unpack +DEPEND=>=sci-biology/bioperl-1.6.9 dev-perl/DBD-mysql dev-perl/DBI sci-biology/biosql dev-perl/Module-Build test? ( dev-perl/Data-Stag dev-perl/Sub-Uplevel dev-perl/Test-Warn dev-perl/Test-Exception virtual/perl-Test-Simple ) dev-lang/perl:=[-build(-)] +DESCRIPTION=Perl tools for bioinformatics - Perl API that accesses the BioSQL schema +EAPI=5 +HOMEPAGE=http://www.bioperl.org/ +IUSE=test +KEYWORDS=amd64 x86 +LICENSE=|| ( Artistic GPL-1+ ) +RDEPEND=>=sci-biology/bioperl-1.6.9 dev-perl/DBD-mysql dev-perl/DBI sci-biology/biosql dev-lang/perl:=[-build(-)] +RESTRICT=test +SLOT=0 +SRC_URI=mirror://cpan/authors/id/C/CJ/CJFIELDS/BioPerl-DB-1.006900.tar.gz +_eclasses_=desktop b1d22ac8bdd4679ab79c71aca235009d epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 1d91b03d42ab6308b5f4f6b598ed110e multiprocessing cac3169468f893670dac3e7cb940e045 perl-functions 6ec4c4d8fc8324200f1c14e8d158c59b perl-module 97206c028d9bdc9f248e022ac5c9fc83 preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c unpacker 3cd8bad0d31e525cd26be1bfa4e61631 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=2470d7ecf1b6ff1902a8d74057748480 diff --git a/metadata/md5-cache/sci-biology/bioperl-db-1.6.9-r1 b/metadata/md5-cache/sci-biology/bioperl-db-1.6.9-r1 new file mode 100644 index 000000000000..aa0828a5f63f --- /dev/null +++ b/metadata/md5-cache/sci-biology/bioperl-db-1.6.9-r1 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile configure install prepare test +DEPEND=>=sci-biology/bioperl-1.6.9 dev-perl/DBD-mysql dev-perl/DBI sci-biology/biosql dev-perl/Module-Build test? ( dev-perl/Data-Stag dev-perl/Sub-Uplevel dev-perl/Test-Warn dev-perl/Test-Exception virtual/perl-Test-Simple ) dev-lang/perl +DESCRIPTION=Perl tools for bioinformatics - Perl API that accesses the BioSQL schema +EAPI=6 +HOMEPAGE=http://www.bioperl.org/ +IUSE=test +KEYWORDS=~amd64 ~x86 +LICENSE=|| ( Artistic GPL-1+ ) +RDEPEND=>=sci-biology/bioperl-1.6.9 dev-perl/DBD-mysql dev-perl/DBI sci-biology/biosql dev-lang/perl:= +RESTRICT=test +SLOT=0 +SRC_URI=mirror://cpan/authors/id/C/CJ/CJFIELDS/BioPerl-DB-1.006900.tar.gz +_eclasses_=multiprocessing cac3169468f893670dac3e7cb940e045 perl-functions 6ec4c4d8fc8324200f1c14e8d158c59b perl-module 97206c028d9bdc9f248e022ac5c9fc83 +_md5_=dbcb977782edcacd68dddedab8e605d9 diff --git a/metadata/md5-cache/sci-biology/bioperl-network-1.6.9 b/metadata/md5-cache/sci-biology/bioperl-network-1.6.9 new file mode 100644 index 000000000000..7bd5e3163500 --- /dev/null +++ b/metadata/md5-cache/sci-biology/bioperl-network-1.6.9 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile configure install prepare test unpack +DEPEND=dev-perl/Module-Build >=sci-biology/bioperl-1.6.9 >=dev-perl/Graph-0.86 dev-lang/perl:=[-build(-)] +DESCRIPTION=Perl tools for bioinformatics - Analysis of protein-protein interaction networks +EAPI=5 +HOMEPAGE=http://www.bioperl.org/ +IUSE=test +KEYWORDS=amd64 x86 +LICENSE=|| ( Artistic GPL-1+ ) +RDEPEND=>=sci-biology/bioperl-1.6.9 >=dev-perl/Graph-0.86 dev-lang/perl:=[-build(-)] +RESTRICT=!test? ( test ) +SLOT=0 +SRC_URI=mirror://cpan/authors/id/C/CJ/CJFIELDS/BioPerl-Network-1.006900.tar.gz +_eclasses_=desktop b1d22ac8bdd4679ab79c71aca235009d epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 1d91b03d42ab6308b5f4f6b598ed110e multiprocessing cac3169468f893670dac3e7cb940e045 perl-functions 6ec4c4d8fc8324200f1c14e8d158c59b perl-module 97206c028d9bdc9f248e022ac5c9fc83 preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c unpacker 3cd8bad0d31e525cd26be1bfa4e61631 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=8f7c4053ffbec76cfad29cca2d99847b diff --git a/metadata/md5-cache/sci-biology/bioperl-run-1.6.9 b/metadata/md5-cache/sci-biology/bioperl-run-1.6.9 new file mode 100644 index 000000000000..1d7140bd3bb3 --- /dev/null +++ b/metadata/md5-cache/sci-biology/bioperl-run-1.6.9 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile configure install prepare test unpack +DEPEND=dev-perl/Module-Build >=sci-biology/bioperl-1.6.9 !minimal? ( dev-perl/Algorithm-Diff dev-perl/XML-Twig dev-perl/IO-String dev-perl/IPC-Run dev-perl/File-Sort ) dev-lang/perl:=[-build(-)] +DESCRIPTION=Perl wrapper modules for key bioinformatics applications +EAPI=5 +HOMEPAGE=http://www.bioperl.org/ +IUSE=-minimal test +KEYWORDS=amd64 x86 +LICENSE=|| ( Artistic GPL-1+ ) +RDEPEND=>=sci-biology/bioperl-1.6.9 !minimal? ( dev-perl/Algorithm-Diff dev-perl/XML-Twig dev-perl/IO-String dev-perl/IPC-Run dev-perl/File-Sort ) dev-lang/perl:=[-build(-)] +RESTRICT=test +SLOT=0 +SRC_URI=mirror://cpan/authors/id/C/CJ/CJFIELDS/BioPerl-Run-1.006900.tar.gz +_eclasses_=desktop b1d22ac8bdd4679ab79c71aca235009d epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 1d91b03d42ab6308b5f4f6b598ed110e multiprocessing cac3169468f893670dac3e7cb940e045 perl-functions 6ec4c4d8fc8324200f1c14e8d158c59b perl-module 97206c028d9bdc9f248e022ac5c9fc83 preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c unpacker 3cd8bad0d31e525cd26be1bfa4e61631 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=9caec4e5b47cbf306a1689903f2a018a diff --git a/metadata/md5-cache/sci-biology/biopython-1.73 b/metadata/md5-cache/sci-biology/biopython-1.73 new file mode 100644 index 000000000000..e24a94a5fc94 --- /dev/null +++ b/metadata/md5-cache/sci-biology/biopython-1.73 @@ -0,0 +1,15 @@ +BDEPEND=python_targets_python3_6? ( dev-lang/python:3.6 ) python_targets_python3_7? ( dev-lang/python:3.7 ) >=dev-lang/python-exec-2:=[python_targets_python3_6(-)?,python_targets_python3_7(-)?,-python_single_target_python3_6(-),-python_single_target_python3_7(-)] dev-python/setuptools[python_targets_python3_6(-)?,python_targets_python3_7(-)?,-python_single_target_python3_6(-),-python_single_target_python3_7(-)] +DEFINED_PHASES=compile configure install postinst prepare test +DEPEND=dev-python/matplotlib[python_targets_python3_6(-)?,python_targets_python3_7(-)?,-python_single_target_python3_6(-),-python_single_target_python3_7(-)] dev-python/networkx[python_targets_python3_6(-)?,python_targets_python3_7(-)?,-python_single_target_python3_6(-),-python_single_target_python3_7(-)] dev-python/numpy[python_targets_python3_6(-)?,python_targets_python3_7(-)?,-python_single_target_python3_6(-),-python_single_target_python3_7(-)] dev-python/rdflib[python_targets_python3_6(-)?,python_targets_python3_7(-)?,-python_single_target_python3_6(-),-python_single_target_python3_7(-)] dev-python/pygraphviz[python_targets_python3_6(-)?,python_targets_python3_7(-)?,-python_single_target_python3_6(-),-python_single_target_python3_7(-)] >=dev-python/reportlab-3.5.13-r1[python_targets_python3_6(-)?,python_targets_python3_7(-)?,-python_single_target_python3_6(-),-python_single_target_python3_7(-)] dev-python/pydot[python_targets_python3_6(-)?,python_targets_python3_7(-)?,-python_single_target_python3_6(-),-python_single_target_python3_7(-)] dev-python/setuptools[python_targets_python3_6(-)?,python_targets_python3_7(-)?,-python_single_target_python3_6(-),-python_single_target_python3_7(-)] sys-devel/flex +DESCRIPTION=Python modules for computational molecular biology +EAPI=7 +HOMEPAGE=https://www.biopython.org/ https://pypi.org/project/biopython/ +IUSE=python_targets_python3_6 python_targets_python3_7 +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux +LICENSE=HPND +RDEPEND=dev-python/matplotlib[python_targets_python3_6(-)?,python_targets_python3_7(-)?,-python_single_target_python3_6(-),-python_single_target_python3_7(-)] dev-python/networkx[python_targets_python3_6(-)?,python_targets_python3_7(-)?,-python_single_target_python3_6(-),-python_single_target_python3_7(-)] dev-python/numpy[python_targets_python3_6(-)?,python_targets_python3_7(-)?,-python_single_target_python3_6(-),-python_single_target_python3_7(-)] dev-python/rdflib[python_targets_python3_6(-)?,python_targets_python3_7(-)?,-python_single_target_python3_6(-),-python_single_target_python3_7(-)] dev-python/pygraphviz[python_targets_python3_6(-)?,python_targets_python3_7(-)?,-python_single_target_python3_6(-),-python_single_target_python3_7(-)] >=dev-python/reportlab-3.5.13-r1[python_targets_python3_6(-)?,python_targets_python3_7(-)?,-python_single_target_python3_6(-),-python_single_target_python3_7(-)] dev-python/pydot[python_targets_python3_6(-)?,python_targets_python3_7(-)?,-python_single_target_python3_6(-),-python_single_target_python3_7(-)] python_targets_python3_6? ( dev-lang/python:3.6 ) python_targets_python3_7? ( dev-lang/python:3.7 ) >=dev-lang/python-exec-2:=[python_targets_python3_6(-)?,python_targets_python3_7(-)?,-python_single_target_python3_6(-),-python_single_target_python3_7(-)] +REQUIRED_USE=|| ( python_targets_python3_6 python_targets_python3_7 ) +SLOT=0 +SRC_URI=mirror://pypi/b/biopython/biopython-1.73.tar.gz +_eclasses_=distutils-r1 c576838cd67e384002a18edd54be710e eutils fcb2aa98e1948b835b5ae66ca52868c5 multibuild 40fe59465edacd730c644ec2bc197809 multilib 1d91b03d42ab6308b5f4f6b598ed110e multiprocessing cac3169468f893670dac3e7cb940e045 python-r1 4eed5e0c72d4544a2291ae46515f5d79 python-utils-r1 611c493a4cfef5254350fabc04b606f5 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c +_md5_=a7d43dcf81616b69a0167851abcbe227 diff --git a/metadata/md5-cache/sci-biology/bioruby-1.5.1 b/metadata/md5-cache/sci-biology/bioruby-1.5.1 new file mode 100644 index 000000000000..56abdcb1c1de --- /dev/null +++ b/metadata/md5-cache/sci-biology/bioruby-1.5.1 @@ -0,0 +1,15 @@ +DEFINED_PHASES=compile configure install prepare setup test unpack +DEPEND=test? ( ruby_targets_ruby24? ( dev-ruby/libxml[ruby_targets_ruby24(-)] ) ) ruby_targets_ruby24? ( dev-lang/ruby:2.4 ) ruby_targets_ruby24? ( doc? ( dev-ruby/rake[ruby_targets_ruby24(-)] ) ) ruby_targets_ruby24? ( test? ( dev-ruby/rake[ruby_targets_ruby24(-)] ) ) ruby_targets_ruby24? ( virtual/rubygems[ruby_targets_ruby24(-)] ) test? ( ruby_targets_ruby24? ( virtual/rubygems[ruby_targets_ruby24(-)] ) ) +DESCRIPTION=An integrated environment for bioinformatics using the Ruby language +EAPI=6 +HOMEPAGE=http://bioruby.org/ +IUSE=test ruby_targets_ruby24 doc test test +KEYWORDS=amd64 ~ppc x86 +LICENSE=Ruby +RDEPEND=ruby_targets_ruby24? ( dev-ruby/libxml[ruby_targets_ruby24(-)] ) ruby_targets_ruby24? ( dev-lang/ruby:2.4 ) ruby_targets_ruby24? ( virtual/rubygems[ruby_targets_ruby24(-)] ) +REQUIRED_USE=|| ( ruby_targets_ruby24 ) +RESTRICT=!test? ( test ) !test? ( test ) !test? ( test ) +SLOT=0 +SRC_URI=https://rubygems.org/gems/bio-1.5.1.gem +_eclasses_=estack 686eaab303305a908fd57b2fd7617800 multilib 1d91b03d42ab6308b5f4f6b598ed110e ruby-fakegem cca036a1477f29b926bf994faddf4099 ruby-ng a1c89995f9f6dd045e93d13a92ca81a9 ruby-utils cdb4c1e4283adb7707b7dd48ccaa7ad2 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c +_md5_=2aecf9a558ab9d1f3e8760530ccd8e56 diff --git a/metadata/md5-cache/sci-biology/bioruby-1.5.2 b/metadata/md5-cache/sci-biology/bioruby-1.5.2 new file mode 100644 index 000000000000..9b08cf8cb53b --- /dev/null +++ b/metadata/md5-cache/sci-biology/bioruby-1.5.2 @@ -0,0 +1,15 @@ +DEFINED_PHASES=compile configure install prepare setup test unpack +DEPEND=test? ( ruby_targets_ruby24? ( dev-ruby/libxml[ruby_targets_ruby24(-)] ) ) ruby_targets_ruby24? ( dev-lang/ruby:2.4 ) ruby_targets_ruby24? ( doc? ( dev-ruby/rake[ruby_targets_ruby24(-)] ) ) ruby_targets_ruby24? ( test? ( dev-ruby/rake[ruby_targets_ruby24(-)] ) ) ruby_targets_ruby24? ( virtual/rubygems[ruby_targets_ruby24(-)] ) test? ( ruby_targets_ruby24? ( virtual/rubygems[ruby_targets_ruby24(-)] ) ) +DESCRIPTION=An integrated environment for bioinformatics using the Ruby language +EAPI=6 +HOMEPAGE=http://bioruby.org/ +IUSE=test ruby_targets_ruby24 doc test test +KEYWORDS=amd64 ~ppc x86 +LICENSE=Ruby +RDEPEND=ruby_targets_ruby24? ( dev-ruby/libxml[ruby_targets_ruby24(-)] ) ruby_targets_ruby24? ( dev-lang/ruby:2.4 ) ruby_targets_ruby24? ( virtual/rubygems[ruby_targets_ruby24(-)] ) +REQUIRED_USE=|| ( ruby_targets_ruby24 ) +RESTRICT=!test? ( test ) !test? ( test ) !test? ( test ) +SLOT=0 +SRC_URI=https://rubygems.org/gems/bio-1.5.2.gem +_eclasses_=estack 686eaab303305a908fd57b2fd7617800 multilib 1d91b03d42ab6308b5f4f6b598ed110e ruby-fakegem cca036a1477f29b926bf994faddf4099 ruby-ng a1c89995f9f6dd045e93d13a92ca81a9 ruby-utils cdb4c1e4283adb7707b7dd48ccaa7ad2 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c +_md5_=4588868f94109a54952cb9e4d284c53d diff --git a/metadata/md5-cache/sci-biology/biosql-1.0.1-r1 b/metadata/md5-cache/sci-biology/biosql-1.0.1-r1 new file mode 100644 index 000000000000..2a7fa17d9aa9 --- /dev/null +++ b/metadata/md5-cache/sci-biology/biosql-1.0.1-r1 @@ -0,0 +1,12 @@ +DEFINED_PHASES=install postinst +DEPEND=mysql? ( dev-perl/DBD-mysql ) postgres? ( dev-perl/DBD-Pg ) +DESCRIPTION=A generic bioinformatics relational database model +EAPI=6 +HOMEPAGE=http://www.biosql.org/ +IUSE=mysql postgres +KEYWORDS=amd64 x86 +LICENSE=LGPL-3 +RDEPEND=mysql? ( dev-perl/DBD-mysql ) postgres? ( dev-perl/DBD-Pg ) dev-lang/perl +SLOT=0 +SRC_URI=http://biosql.org/DIST/biosql-1.0.1.tar.bz2 +_md5_=c3363146ed9daed7fd12e748db91abe0 diff --git a/metadata/md5-cache/sci-biology/blat-34-r2 b/metadata/md5-cache/sci-biology/blat-34-r2 new file mode 100644 index 000000000000..d29c9e0cf9cf --- /dev/null +++ b/metadata/md5-cache/sci-biology/blat-34-r2 @@ -0,0 +1,11 @@ +DEFINED_PHASES=compile install +DEPEND=app-arch/unzip +DESCRIPTION=The BLAST-Like Alignment Tool, a fast genomic sequence aligner +EAPI=6 +HOMEPAGE=http://www.cse.ucsc.edu/~kent/ +KEYWORDS=~amd64 ~x86 +LICENSE=blat +SLOT=0 +SRC_URI=http://www.soe.ucsc.edu/~kent/src/blatSrc34.zip +_eclasses_=multilib 1d91b03d42ab6308b5f4f6b598ed110e toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c +_md5_=d48361335699038107318f5ca57533e8 diff --git a/metadata/md5-cache/sci-biology/bowtie-1.1.2-r1 b/metadata/md5-cache/sci-biology/bowtie-1.1.2-r1 new file mode 100644 index 000000000000..504c8633fd6f --- /dev/null +++ b/metadata/md5-cache/sci-biology/bowtie-1.1.2-r1 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile install prepare +DEPEND=tbb? ( dev-cpp/tbb ) sci-biology/seqan:1.4 app-arch/unzip +DESCRIPTION=Popular short read aligner for Next-generation sequencing data +EAPI=6 +HOMEPAGE=http://bowtie-bio.sourceforge.net/ +IUSE=examples +tbb +KEYWORDS=~amd64 ~x86 ~x64-macos +LICENSE=Artistic +RDEPEND=tbb? ( dev-cpp/tbb ) +SLOT=1 +SRC_URI=mirror://sourceforge/bowtie-bio/bowtie-1.1.2-src.zip +_eclasses_=desktop b1d22ac8bdd4679ab79c71aca235009d epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 flag-o-matic dc34234e8c43343da45853da22dcf14b ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 1d91b03d42ab6308b5f4f6b598ed110e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=069dc133bc01cabadeda1e327034b7a7 diff --git a/metadata/md5-cache/sci-biology/bowtie-2.2.9 b/metadata/md5-cache/sci-biology/bowtie-2.2.9 new file mode 100644 index 000000000000..5ff5336f3003 --- /dev/null +++ b/metadata/md5-cache/sci-biology/bowtie-2.2.9 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile install pretend +DEPEND=dev-lang/perl tbb? ( dev-cpp/tbb ) app-arch/unzip +DESCRIPTION=Popular short read aligner for Next-generation sequencing data +EAPI=6 +HOMEPAGE=http://bowtie-bio.sourceforge.net/bowtie2/ +IUSE=examples cpu_flags_x86_sse2 +tbb +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-3 +RDEPEND=dev-lang/perl tbb? ( dev-cpp/tbb ) +SLOT=2 +SRC_URI=mirror://sourceforge/project/bowtie-bio/bowtie2/2.2.9/bowtie2-2.2.9-source.zip +_eclasses_=multilib 1d91b03d42ab6308b5f4f6b598ed110e toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c +_md5_=46d87c867cd445707dc1913cf3dd7eb6 diff --git a/metadata/md5-cache/sci-biology/bwa-0.7.16a b/metadata/md5-cache/sci-biology/bwa-0.7.16a new file mode 100644 index 000000000000..ba3e4ad14795 --- /dev/null +++ b/metadata/md5-cache/sci-biology/bwa-0.7.16a @@ -0,0 +1,11 @@ +DEFINED_PHASES=configure install +DESCRIPTION=Burrows-Wheeler Alignment Tool, a fast short genomic sequence aligner +EAPI=7 +HOMEPAGE=https://bio-bwa.sourceforge.net/ +KEYWORDS=~amd64 ~x86 ~x64-macos +LICENSE=GPL-3 +RDEPEND=dev-lang/perl +SLOT=0 +SRC_URI=mirror://sourceforge/bio-bwa/bwa-0.7.16a.tar.bz2 +_eclasses_=multilib 1d91b03d42ab6308b5f4f6b598ed110e toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c +_md5_=6b21049857f301168f361c45510f8256 diff --git a/metadata/md5-cache/sci-biology/cd-hit-4.6.6 b/metadata/md5-cache/sci-biology/cd-hit-4.6.6 new file mode 100644 index 000000000000..355592f7e2e6 --- /dev/null +++ b/metadata/md5-cache/sci-biology/cd-hit-4.6.6 @@ -0,0 +1,12 @@ +DEFINED_PHASES=compile install pretend setup +DESCRIPTION=Clustering Database at High Identity with Tolerance +EAPI=6 +HOMEPAGE=http://weizhong-lab.ucsd.edu/cd-hit/ +IUSE=openmp +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux +LICENSE=GPL-2 +RDEPEND=dev-lang/perl +SLOT=0 +SRC_URI=https://github.com/weizhongli/cdhit/releases/download/V4.6.6/cd-hit-v4.6.6-2016-0711.tar.gz -> cd-hit-4.6.6.tar.gz +_eclasses_=desktop b1d22ac8bdd4679ab79c71aca235009d epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 flag-o-matic dc34234e8c43343da45853da22dcf14b ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 1d91b03d42ab6308b5f4f6b598ed110e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=bbe0ae10275a73485487e08f19f4ac1b diff --git a/metadata/md5-cache/sci-biology/clustal-omega-1.2.4 b/metadata/md5-cache/sci-biology/clustal-omega-1.2.4 new file mode 100644 index 000000000000..fe4180c6523a --- /dev/null +++ b/metadata/md5-cache/sci-biology/clustal-omega-1.2.4 @@ -0,0 +1,13 @@ +DEFINED_PHASES=configure install prepare +DEPEND=dev-libs/argtable >=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 +DESCRIPTION=Scalable multiple alignment of protein sequences +EAPI=6 +HOMEPAGE=http://www.clustal.org/omega/ +IUSE=static-libs +KEYWORDS=amd64 x86 +LICENSE=GPL-2 +RDEPEND=dev-libs/argtable +SLOT=0 +SRC_URI=http://www.clustal.org/omega/clustal-omega-1.2.4.tar.gz +_eclasses_=autotools ea7865c8fba1ea8d3639f355fffe1a3c libtool f143db5a74ccd9ca28c1234deffede96 multilib 1d91b03d42ab6308b5f4f6b598ed110e toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c +_md5_=9ade45d2e283bc5fcc7eef16725e18ae diff --git a/metadata/md5-cache/sci-biology/clustalw-1.83-r4 b/metadata/md5-cache/sci-biology/clustalw-1.83-r4 new file mode 100644 index 000000000000..94ab1984ace1 --- /dev/null +++ b/metadata/md5-cache/sci-biology/clustalw-1.83-r4 @@ -0,0 +1,10 @@ +DEFINED_PHASES=install prepare +DESCRIPTION=General purpose multiple alignment program for DNA and proteins +EAPI=6 +HOMEPAGE=http://www.embl-heidelberg.de/~seqanal/ +KEYWORDS=~alpha amd64 ppc ppc64 sparc x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris +LICENSE=clustalw +SLOT=1 +SRC_URI=ftp://ftp.ebi.ac.uk/pub/software/unix/clustalw/clustalw1.83.UNIX.tar.gz +_eclasses_=multilib 1d91b03d42ab6308b5f4f6b598ed110e toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c +_md5_=9b185c4d48718080d0ef7b95b7c9533d diff --git a/metadata/md5-cache/sci-biology/clustalw-2.1-r1 b/metadata/md5-cache/sci-biology/clustalw-2.1-r1 new file mode 100644 index 000000000000..5e8138428bfc --- /dev/null +++ b/metadata/md5-cache/sci-biology/clustalw-2.1-r1 @@ -0,0 +1,9 @@ +DEFINED_PHASES=install +DESCRIPTION=General purpose multiple alignment program for DNA and proteins +EAPI=6 +HOMEPAGE=http://www.clustal.org/ +KEYWORDS=amd64 x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris +LICENSE=GPL-3 LGPL-3 +SLOT=2 +SRC_URI=http://www.clustal.org/download/current/clustalw-2.1.tar.gz +_md5_=397de2c00339f3a0b847f6daa9a481fb diff --git a/metadata/md5-cache/sci-biology/clustalw-mpi-0.13-r2 b/metadata/md5-cache/sci-biology/clustalw-mpi-0.13-r2 new file mode 100644 index 000000000000..c2887dc489f6 --- /dev/null +++ b/metadata/md5-cache/sci-biology/clustalw-mpi-0.13-r2 @@ -0,0 +1,13 @@ +DEFINED_PHASES=install prepare +DEPEND=virtual/mpi +DESCRIPTION=An MPI implemention of the ClustalW general purpose multiple alignment algorithm +EAPI=6 +HOMEPAGE=http://www.bii.a-star.edu.sg/achievements/applications/clustalw/index.php +IUSE=mpi_njtree static_pairalign +KEYWORDS=~amd64 ~x86 +LICENSE=public-domain +RDEPEND=virtual/mpi +SLOT=0 +SRC_URI=http://web.bii.a-star.edu.sg/~kuobin/clustalw-mpi/clustalw-mpi-0.13.tar.gz +_eclasses_=multilib 1d91b03d42ab6308b5f4f6b598ed110e toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c +_md5_=9e376a1d2ae782d9495b0c6c318aa097 diff --git a/metadata/md5-cache/sci-biology/clustalx-2.1-r3 b/metadata/md5-cache/sci-biology/clustalx-2.1-r3 new file mode 100644 index 000000000000..4ee69ccc58a1 --- /dev/null +++ b/metadata/md5-cache/sci-biology/clustalx-2.1-r3 @@ -0,0 +1,12 @@ +DEFINED_PHASES=configure install prepare +DEPEND=dev-qt/qtcore:5 dev-qt/qtgui:5 dev-qt/qtwidgets:5 dev-qt/qtxml:5 +DESCRIPTION=Graphical interface for the ClustalW multiple alignment program +EAPI=6 +HOMEPAGE=http://www.ebi.ac.uk/tools/clustalw2/ +KEYWORDS=amd64 x86 +LICENSE=GPL-3 LGPL-3 +RDEPEND=dev-qt/qtcore:5 dev-qt/qtgui:5 dev-qt/qtwidgets:5 dev-qt/qtxml:5 >=sci-biology/clustalw-2.1 +SLOT=0 +SRC_URI=http://www.clustal.org/download/current/clustalx-2.1.tar.gz https://dev.gentoo.org/~jlec/distfiles/clustalx.png.xz +_eclasses_=desktop b1d22ac8bdd4679ab79c71aca235009d estack 686eaab303305a908fd57b2fd7617800 multilib 1d91b03d42ab6308b5f4f6b598ed110e qmake-utils 4eb5e05ef7ee630c003e3f0edc094135 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c +_md5_=c8dbd602c40010526edb4955aa67e1b3 diff --git a/metadata/md5-cache/sci-biology/consed-29 b/metadata/md5-cache/sci-biology/consed-29 new file mode 100644 index 000000000000..d9555343ca6c --- /dev/null +++ b/metadata/md5-cache/sci-biology/consed-29 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile configure install nofetch postinst prepare +DEPEND=x11-libs/libX11 x11-libs/motif:0 sci-biology/samtools:0.1-legacy virtual/pkgconfig +DESCRIPTION=A genome sequence finishing program +EAPI=6 +HOMEPAGE=http://bozeman.mbt.washington.edu/consed/consed.html +IUSE=examples +KEYWORDS=~amd64 ~x86 +LICENSE=phrap +RDEPEND=x11-libs/libX11 x11-libs/motif:0 sci-biology/samtools:0.1-legacy dev-lang/perl >=sci-biology/phred-071220-r1 >=sci-biology/phrap-1.080812-r2 +RESTRICT=fetch +SLOT=0 +SRC_URI=consed-29-sources.tar.gz consed-29-linux.tar.gz +_eclasses_=desktop b1d22ac8bdd4679ab79c71aca235009d epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 flag-o-matic dc34234e8c43343da45853da22dcf14b ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 1d91b03d42ab6308b5f4f6b598ed110e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=1e30f1827727dab34c75c8c026745369 diff --git a/metadata/md5-cache/sci-biology/cutg-160-r1 b/metadata/md5-cache/sci-biology/cutg-160-r1 new file mode 100644 index 000000000000..60c35396bc6a --- /dev/null +++ b/metadata/md5-cache/sci-biology/cutg-160-r1 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile install +DEPEND=emboss? ( sci-biology/emboss ) +DESCRIPTION=Codon usage tables calculated from GenBank +EAPI=5 +HOMEPAGE=http://www.kazusa.or.jp/codon/ +IUSE=emboss minimal +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux +LICENSE=public-domain +RDEPEND=emboss? ( sci-biology/emboss ) +RESTRICT=binchecks strip +SLOT=0 +SRC_URI=https://dev.gentoo.org/~jlec/distfiles/cutg-160.tar.xz +_md5_=bbbd347ac6eafe2416778cd68a45bf1a diff --git a/metadata/md5-cache/sci-biology/dialign-tx-1.0.2-r2 b/metadata/md5-cache/sci-biology/dialign-tx-1.0.2-r2 new file mode 100644 index 000000000000..8582388a108d --- /dev/null +++ b/metadata/md5-cache/sci-biology/dialign-tx-1.0.2-r2 @@ -0,0 +1,10 @@ +DEFINED_PHASES=compile configure install postinst +DESCRIPTION=Greedy and progressive approaches for segment-based multiple sequence alignment +EAPI=6 +HOMEPAGE=http://dialign-tx.gobics.de/ +KEYWORDS=~amd64 ~x86 +LICENSE=LGPL-2.1 +SLOT=0 +SRC_URI=http://dialign-tx.gobics.de/DIALIGN-TX_1.0.2.tar.gz +_eclasses_=multilib 1d91b03d42ab6308b5f4f6b598ed110e toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c +_md5_=b04d9beffea802bb82f896df101ca660 diff --git a/metadata/md5-cache/sci-biology/dialign2-2.2.1 b/metadata/md5-cache/sci-biology/dialign2-2.2.1 new file mode 100644 index 000000000000..6e57a472a0b6 --- /dev/null +++ b/metadata/md5-cache/sci-biology/dialign2-2.2.1 @@ -0,0 +1,10 @@ +DEFINED_PHASES=compile configure install +DESCRIPTION=Multiple sequence alignment +EAPI=6 +HOMEPAGE=http://bibiserv.techfak.uni-bielefeld.de/dialign +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux +LICENSE=LGPL-2.1 +SLOT=0 +SRC_URI=http://bibiserv.techfak.uni-bielefeld.de/applications/dialign/resources/downloads/dialign-2.2.1-src.tar.gz +_eclasses_=desktop b1d22ac8bdd4679ab79c71aca235009d epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 flag-o-matic dc34234e8c43343da45853da22dcf14b ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 1d91b03d42ab6308b5f4f6b598ed110e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=3761a69a47f38308f54ae0b051361ed6 diff --git a/metadata/md5-cache/sci-biology/diya-1.0_rc4 b/metadata/md5-cache/sci-biology/diya-1.0_rc4 new file mode 100644 index 000000000000..05cbb098f0b2 --- /dev/null +++ b/metadata/md5-cache/sci-biology/diya-1.0_rc4 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile configure install prepare test unpack +DEPEND=sci-biology/bioperl dev-perl/Data-Utilities dev-perl/XML-Simple dev-lang/perl:=[-build(-)] +DESCRIPTION=Do It Yourself Annotation, tools & libraries for sequence assembly & annotation +EAPI=5 +HOMEPAGE=http://gmod.org/wiki/Diya +IUSE=-minimal +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-3 +RDEPEND=sci-biology/bioperl dev-perl/Data-Utilities dev-perl/XML-Simple !minimal? ( sci-biology/mummer sci-biology/glimmer sci-biology/trnascan-se sci-biology/infernal ) dev-lang/perl:=[-build(-)] +SLOT=0 +SRC_URI=mirror://sourceforge/diyg/files/diya/diya-1.0/diya-1.0-rc4.tar.gz +_eclasses_=desktop b1d22ac8bdd4679ab79c71aca235009d epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 1d91b03d42ab6308b5f4f6b598ed110e multiprocessing cac3169468f893670dac3e7cb940e045 perl-functions 6ec4c4d8fc8324200f1c14e8d158c59b perl-module 97206c028d9bdc9f248e022ac5c9fc83 preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c unpacker 3cd8bad0d31e525cd26be1bfa4e61631 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=5d4639d7c08c43e2c2208492508fd56c diff --git a/metadata/md5-cache/sci-biology/elph-1.0.1-r1 b/metadata/md5-cache/sci-biology/elph-1.0.1-r1 new file mode 100644 index 000000000000..824a1a7acc99 --- /dev/null +++ b/metadata/md5-cache/sci-biology/elph-1.0.1-r1 @@ -0,0 +1,10 @@ +DEFINED_PHASES=configure install +DESCRIPTION=Estimated Locations of Pattern Hits - Motif finder program +EAPI=6 +HOMEPAGE=http://cbcb.umd.edu/software/ELPH/ +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos +LICENSE=Artistic +SLOT=0 +SRC_URI=ftp://ftp.cbcb.umd.edu/pub/software/elph/ELPH-1.0.1.tar.gz +_eclasses_=multilib 1d91b03d42ab6308b5f4f6b598ed110e toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c +_md5_=dbee2f511488caf9eadadb20d043a2da diff --git a/metadata/md5-cache/sci-biology/embassy-6.6.0-r1 b/metadata/md5-cache/sci-biology/embassy-6.6.0-r1 new file mode 100644 index 000000000000..b4d67ce54ddb --- /dev/null +++ b/metadata/md5-cache/sci-biology/embassy-6.6.0-r1 @@ -0,0 +1,9 @@ +DEFINED_PHASES=- +DESCRIPTION=A meta-package for installing all EMBASSY packages (EMBOSS add-ons) +EAPI=6 +HOMEPAGE=http://emboss.sourceforge.net/embassy/ +KEYWORDS=~amd64 ~x86 ~x86-linux +LICENSE=metapackage +RDEPEND=>=sci-biology/embassy-cbstools-1.0.0.660 >=sci-biology/embassy-clustalomega-1.1.0.660 >=sci-biology/embassy-domainatrix-0.1.660 >=sci-biology/embassy-domalign-0.1.660 >=sci-biology/embassy-domsearch-0.1.660 >=sci-biology/embassy-emnu-1.05.660 >=sci-biology/embassy-esim4-1.0.0.660 >=sci-biology/embassy-hmmer-2.3.2.660 >=sci-biology/embassy-iprscan-4.3.1.660 >=sci-biology/embassy-meme-4.7.660 >=sci-biology/embassy-mse-3.0.0.660 >=sci-biology/embassy-phylipnew-3.69.660 >=sci-biology/embassy-signature-0.1.660 >=sci-biology/embassy-structure-0.1.660 >=sci-biology/embassy-topo-2.0.660 >=sci-biology/embassy-vienna-1.7.2.660 +SLOT=0 +_md5_=0b1857c92d1042b678e6eab58eda3420 diff --git a/metadata/md5-cache/sci-biology/embassy-cbstools-1.0.0.660 b/metadata/md5-cache/sci-biology/embassy-cbstools-1.0.0.660 new file mode 100644 index 000000000000..bb261a603661 --- /dev/null +++ b/metadata/md5-cache/sci-biology/embassy-cbstools-1.0.0.660 @@ -0,0 +1,13 @@ +DEFINED_PHASES=configure install prepare +DEPEND=>=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( dev-db/mysql-connector-c:0= ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] +DESCRIPTION=EMBOSS integrated version of Applications from the CBS group +EAPI=6 +HOMEPAGE=http://emboss.sourceforge.net/ +IUSE=mysql pdf png postgres static-libs X +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux +LICENSE=LGPL-2 GPL-2 +RDEPEND=dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( dev-db/mysql-connector-c:0= ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] +SLOT=0 +SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/CBSTOOLS-1.0.0.660.tar.gz -> embassy-cbstools-1.0.0.660.tar.gz +_eclasses_=autotools ea7865c8fba1ea8d3639f355fffe1a3c desktop b1d22ac8bdd4679ab79c71aca235009d emboss-r2 4cc77fdd8beda583053fe8bf1a2cc8a5 epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 flag-o-matic dc34234e8c43343da45853da22dcf14b libtool f143db5a74ccd9ca28c1234deffede96 ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 1d91b03d42ab6308b5f4f6b598ed110e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=4166ba28131fdf70907b31300aa4c08b diff --git a/metadata/md5-cache/sci-biology/embassy-clustalomega-1.1.0.660 b/metadata/md5-cache/sci-biology/embassy-clustalomega-1.1.0.660 new file mode 100644 index 000000000000..bdfb37337e4f --- /dev/null +++ b/metadata/md5-cache/sci-biology/embassy-clustalomega-1.1.0.660 @@ -0,0 +1,13 @@ +DEFINED_PHASES=configure install prepare +DEPEND=>=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( dev-db/mysql-connector-c:0= ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] +DESCRIPTION=EMBOSS integrated version of Clustal Omega - Multiple Sequence Alignment +EAPI=6 +HOMEPAGE=http://emboss.sourceforge.net/ +IUSE=mysql pdf png postgres static-libs X +KEYWORDS=~amd64 ~x86 ~x86-linux +LICENSE=LGPL-2 GPL-2 +RDEPEND=sci-biology/clustal-omega dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( dev-db/mysql-connector-c:0= ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] +SLOT=0 +SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/CLUSTALOMEGA-1.1.0.660.tar.gz -> embassy-clustalomega-1.1.0.660.tar.gz +_eclasses_=autotools ea7865c8fba1ea8d3639f355fffe1a3c desktop b1d22ac8bdd4679ab79c71aca235009d emboss-r2 4cc77fdd8beda583053fe8bf1a2cc8a5 epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 flag-o-matic dc34234e8c43343da45853da22dcf14b libtool f143db5a74ccd9ca28c1234deffede96 ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 1d91b03d42ab6308b5f4f6b598ed110e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=ef491b452e56be12961f62b16961f4f1 diff --git a/metadata/md5-cache/sci-biology/embassy-domainatrix-0.1.660 b/metadata/md5-cache/sci-biology/embassy-domainatrix-0.1.660 new file mode 100644 index 000000000000..92f8fee4dcae --- /dev/null +++ b/metadata/md5-cache/sci-biology/embassy-domainatrix-0.1.660 @@ -0,0 +1,13 @@ +DEFINED_PHASES=configure install prepare +DEPEND=>=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( dev-db/mysql-connector-c:0= ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] +DESCRIPTION=EMBOSS integrated version of Protein domain analysis add-on package +EAPI=6 +HOMEPAGE=http://emboss.sourceforge.net/ +IUSE=mysql pdf png postgres static-libs X +KEYWORDS=~amd64 ~x86 ~x86-linux +LICENSE=LGPL-2 GPL-2 +RDEPEND=dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( dev-db/mysql-connector-c:0= ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] +SLOT=0 +SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/DOMAINATRIX-0.1.660.tar.gz -> embassy-domainatrix-0.1.660.tar.gz +_eclasses_=autotools ea7865c8fba1ea8d3639f355fffe1a3c desktop b1d22ac8bdd4679ab79c71aca235009d emboss-r2 4cc77fdd8beda583053fe8bf1a2cc8a5 epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 flag-o-matic dc34234e8c43343da45853da22dcf14b libtool f143db5a74ccd9ca28c1234deffede96 ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 1d91b03d42ab6308b5f4f6b598ed110e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=bfee4f5b2b2adadb41de2eb02d4dcbc0 diff --git a/metadata/md5-cache/sci-biology/embassy-domalign-0.1.660 b/metadata/md5-cache/sci-biology/embassy-domalign-0.1.660 new file mode 100644 index 000000000000..dbae71e62e7f --- /dev/null +++ b/metadata/md5-cache/sci-biology/embassy-domalign-0.1.660 @@ -0,0 +1,13 @@ +DEFINED_PHASES=configure install prepare +DEPEND=>=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( dev-db/mysql-connector-c:0= ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] +DESCRIPTION=EMBOSS integrated version of Protein domain alignment add-on package +EAPI=6 +HOMEPAGE=http://emboss.sourceforge.net/ +IUSE=mysql pdf png postgres static-libs X +KEYWORDS=~amd64 ~x86 ~x86-linux +LICENSE=LGPL-2 GPL-2 +RDEPEND=dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( dev-db/mysql-connector-c:0= ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] +SLOT=0 +SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/DOMALIGN-0.1.660.tar.gz -> embassy-domalign-0.1.660.tar.gz +_eclasses_=autotools ea7865c8fba1ea8d3639f355fffe1a3c desktop b1d22ac8bdd4679ab79c71aca235009d emboss-r2 4cc77fdd8beda583053fe8bf1a2cc8a5 epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 flag-o-matic dc34234e8c43343da45853da22dcf14b libtool f143db5a74ccd9ca28c1234deffede96 ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 1d91b03d42ab6308b5f4f6b598ed110e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=9f8b2caa273f4ae3b0463e6de6782660 diff --git a/metadata/md5-cache/sci-biology/embassy-domsearch-0.1.660 b/metadata/md5-cache/sci-biology/embassy-domsearch-0.1.660 new file mode 100644 index 000000000000..7a2180915455 --- /dev/null +++ b/metadata/md5-cache/sci-biology/embassy-domsearch-0.1.660 @@ -0,0 +1,13 @@ +DEFINED_PHASES=configure install prepare +DEPEND=>=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( dev-db/mysql-connector-c:0= ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] +DESCRIPTION=EMBOSS integrated version of Protein domain search add-on package +EAPI=6 +HOMEPAGE=http://emboss.sourceforge.net/ +IUSE=mysql pdf png postgres static-libs X +KEYWORDS=~amd64 ~x86 ~x86-linux +LICENSE=LGPL-2 GPL-2 +RDEPEND=dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( dev-db/mysql-connector-c:0= ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] +SLOT=0 +SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/DOMSEARCH-0.1.660.tar.gz -> embassy-domsearch-0.1.660.tar.gz +_eclasses_=autotools ea7865c8fba1ea8d3639f355fffe1a3c desktop b1d22ac8bdd4679ab79c71aca235009d emboss-r2 4cc77fdd8beda583053fe8bf1a2cc8a5 epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 flag-o-matic dc34234e8c43343da45853da22dcf14b libtool f143db5a74ccd9ca28c1234deffede96 ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 1d91b03d42ab6308b5f4f6b598ed110e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=920906439fbc5278460201b23a615736 diff --git a/metadata/md5-cache/sci-biology/embassy-emnu-1.05.660 b/metadata/md5-cache/sci-biology/embassy-emnu-1.05.660 new file mode 100644 index 000000000000..a5aa2a31eee0 --- /dev/null +++ b/metadata/md5-cache/sci-biology/embassy-emnu-1.05.660 @@ -0,0 +1,13 @@ +DEFINED_PHASES=configure install prepare +DEPEND=>=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( dev-db/mysql-connector-c:0= ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] +DESCRIPTION=EMBOSS integrated version of Simple menu of EMBOSS applications +EAPI=6 +HOMEPAGE=http://emboss.sourceforge.net/ +IUSE=ncurses mysql pdf png postgres static-libs X +KEYWORDS=~amd64 ~x86 ~x86-linux +LICENSE=LGPL-2 GPL-2 +RDEPEND=ncurses? ( sys-libs/ncurses:0= ) dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( dev-db/mysql-connector-c:0= ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] +SLOT=0 +SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/EMNU-1.05.660.tar.gz -> embassy-emnu-1.05.660.tar.gz +_eclasses_=autotools ea7865c8fba1ea8d3639f355fffe1a3c desktop b1d22ac8bdd4679ab79c71aca235009d emboss-r2 4cc77fdd8beda583053fe8bf1a2cc8a5 epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 flag-o-matic dc34234e8c43343da45853da22dcf14b libtool f143db5a74ccd9ca28c1234deffede96 ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 1d91b03d42ab6308b5f4f6b598ed110e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=d82c7c44ec76fa5d6165769a73e5df9a diff --git a/metadata/md5-cache/sci-biology/embassy-esim4-1.0.0.660 b/metadata/md5-cache/sci-biology/embassy-esim4-1.0.0.660 new file mode 100644 index 000000000000..4ddad9347c28 --- /dev/null +++ b/metadata/md5-cache/sci-biology/embassy-esim4-1.0.0.660 @@ -0,0 +1,13 @@ +DEFINED_PHASES=configure install prepare +DEPEND=>=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( dev-db/mysql-connector-c:0= ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] +DESCRIPTION=EMBOSS integrated version of sim4 - Alignment of cDNA and genomic DNA +EAPI=6 +HOMEPAGE=http://emboss.sourceforge.net/ +IUSE=mysql pdf png postgres static-libs X +KEYWORDS=~amd64 ~x86 ~x86-linux +LICENSE=LGPL-2 GPL-2 +RDEPEND=dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( dev-db/mysql-connector-c:0= ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] +SLOT=0 +SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/ESIM4-1.0.0.660.tar.gz -> embassy-esim4-1.0.0.660.tar.gz +_eclasses_=autotools ea7865c8fba1ea8d3639f355fffe1a3c desktop b1d22ac8bdd4679ab79c71aca235009d emboss-r2 4cc77fdd8beda583053fe8bf1a2cc8a5 epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 flag-o-matic dc34234e8c43343da45853da22dcf14b libtool f143db5a74ccd9ca28c1234deffede96 ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 1d91b03d42ab6308b5f4f6b598ed110e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=1b156bed7ea031aeb5464836dd987f18 diff --git a/metadata/md5-cache/sci-biology/embassy-hmmer-2.3.2.660 b/metadata/md5-cache/sci-biology/embassy-hmmer-2.3.2.660 new file mode 100644 index 000000000000..11217b8f8abb --- /dev/null +++ b/metadata/md5-cache/sci-biology/embassy-hmmer-2.3.2.660 @@ -0,0 +1,13 @@ +DEFINED_PHASES=configure install prepare +DEPEND=>=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( dev-db/mysql-connector-c:0= ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] +DESCRIPTION=EMBOSS integrated version of HMMER wrapper - sequence analysis with profile HMMs +EAPI=6 +HOMEPAGE=http://emboss.sourceforge.net/ +IUSE=mysql pdf png postgres static-libs X +KEYWORDS=~amd64 ~x86 ~x86-linux +LICENSE=LGPL-2 GPL-2 +RDEPEND=sci-biology/hmmer:2 dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( dev-db/mysql-connector-c:0= ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] +SLOT=0 +SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/HMMER-2.3.2.660.tar.gz -> embassy-hmmer-2.3.2.660.tar.gz +_eclasses_=autotools ea7865c8fba1ea8d3639f355fffe1a3c desktop b1d22ac8bdd4679ab79c71aca235009d emboss-r2 4cc77fdd8beda583053fe8bf1a2cc8a5 epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 flag-o-matic dc34234e8c43343da45853da22dcf14b libtool f143db5a74ccd9ca28c1234deffede96 ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 1d91b03d42ab6308b5f4f6b598ed110e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=83d02ae22d4e1864669639d9289cd112 diff --git a/metadata/md5-cache/sci-biology/embassy-iprscan-4.3.1.660 b/metadata/md5-cache/sci-biology/embassy-iprscan-4.3.1.660 new file mode 100644 index 000000000000..2f39aeea1724 --- /dev/null +++ b/metadata/md5-cache/sci-biology/embassy-iprscan-4.3.1.660 @@ -0,0 +1,13 @@ +DEFINED_PHASES=configure install prepare +DEPEND=>=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( dev-db/mysql-connector-c:0= ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] +DESCRIPTION=EMBOSS integrated version of InterProScan motif detection add-on package +EAPI=6 +HOMEPAGE=http://emboss.sourceforge.net/ +IUSE=mysql pdf png postgres static-libs X +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux +LICENSE=LGPL-2 GPL-2 +RDEPEND=dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( dev-db/mysql-connector-c:0= ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] +SLOT=0 +SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/IPRSCAN-4.3.1.660.tar.gz -> embassy-iprscan-4.3.1.660.tar.gz +_eclasses_=autotools ea7865c8fba1ea8d3639f355fffe1a3c desktop b1d22ac8bdd4679ab79c71aca235009d emboss-r2 4cc77fdd8beda583053fe8bf1a2cc8a5 epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 flag-o-matic dc34234e8c43343da45853da22dcf14b libtool f143db5a74ccd9ca28c1234deffede96 ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 1d91b03d42ab6308b5f4f6b598ed110e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=73b0c29964ea3506d18ef6b6c8df70e1 diff --git a/metadata/md5-cache/sci-biology/embassy-meme-4.7.660 b/metadata/md5-cache/sci-biology/embassy-meme-4.7.660 new file mode 100644 index 000000000000..302b41f8d32f --- /dev/null +++ b/metadata/md5-cache/sci-biology/embassy-meme-4.7.660 @@ -0,0 +1,13 @@ +DEFINED_PHASES=configure install prepare +DEPEND=>=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( dev-db/mysql-connector-c:0= ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] +DESCRIPTION=EMBOSS integrated version of MEME - Multiple Em for Motif Elicitation +EAPI=6 +HOMEPAGE=http://emboss.sourceforge.net/ +IUSE=mysql pdf png postgres static-libs X +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux +LICENSE=LGPL-2 GPL-2 +RDEPEND=sci-biology/meme dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( dev-db/mysql-connector-c:0= ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] +SLOT=0 +SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/MEME-4.7.660.tar.gz -> embassy-meme-4.7.660.tar.gz +_eclasses_=autotools ea7865c8fba1ea8d3639f355fffe1a3c desktop b1d22ac8bdd4679ab79c71aca235009d emboss-r2 4cc77fdd8beda583053fe8bf1a2cc8a5 epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 flag-o-matic dc34234e8c43343da45853da22dcf14b libtool f143db5a74ccd9ca28c1234deffede96 ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 1d91b03d42ab6308b5f4f6b598ed110e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=b18db6d7a2159272c7b69d34a14dc9b5 diff --git a/metadata/md5-cache/sci-biology/embassy-mse-3.0.0.660 b/metadata/md5-cache/sci-biology/embassy-mse-3.0.0.660 new file mode 100644 index 000000000000..c23cf1f9b28e --- /dev/null +++ b/metadata/md5-cache/sci-biology/embassy-mse-3.0.0.660 @@ -0,0 +1,13 @@ +DEFINED_PHASES=configure install prepare +DEPEND=>=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( dev-db/mysql-connector-c:0= ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] +DESCRIPTION=EMBOSS integrated version of MSE - Multiple Sequence Screen Editor +EAPI=6 +HOMEPAGE=http://emboss.sourceforge.net/ +IUSE=ncurses mysql pdf png postgres static-libs X +KEYWORDS=~amd64 ~x86 ~x86-linux +LICENSE=LGPL-2 GPL-2 +RDEPEND=ncurses? ( sys-libs/ncurses:0= ) dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( dev-db/mysql-connector-c:0= ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] +SLOT=0 +SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/MSE-3.0.0.660.tar.gz -> embassy-mse-3.0.0.660.tar.gz +_eclasses_=autotools ea7865c8fba1ea8d3639f355fffe1a3c desktop b1d22ac8bdd4679ab79c71aca235009d emboss-r2 4cc77fdd8beda583053fe8bf1a2cc8a5 epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 flag-o-matic dc34234e8c43343da45853da22dcf14b libtool f143db5a74ccd9ca28c1234deffede96 ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 1d91b03d42ab6308b5f4f6b598ed110e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=84df94b7c4b0f044de45cef524cbf453 diff --git a/metadata/md5-cache/sci-biology/embassy-phylipnew-3.69.660 b/metadata/md5-cache/sci-biology/embassy-phylipnew-3.69.660 new file mode 100644 index 000000000000..9016d9b1caaf --- /dev/null +++ b/metadata/md5-cache/sci-biology/embassy-phylipnew-3.69.660 @@ -0,0 +1,13 @@ +DEFINED_PHASES=configure install prepare +DEPEND=>=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( dev-db/mysql-connector-c:0= ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] +DESCRIPTION=EMBOSS integrated version of The Phylogeny Inference Package +EAPI=6 +HOMEPAGE=http://emboss.sourceforge.net/ +IUSE=mysql pdf png postgres static-libs X +KEYWORDS=~amd64 ~x86 ~x86-linux +LICENSE=LGPL-2 GPL-2 free-noncomm +RDEPEND=dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( dev-db/mysql-connector-c:0= ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] +SLOT=0 +SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/PHYLIPNEW-3.69.660.tar.gz -> embassy-phylipnew-3.69.660.tar.gz +_eclasses_=autotools ea7865c8fba1ea8d3639f355fffe1a3c desktop b1d22ac8bdd4679ab79c71aca235009d emboss-r2 4cc77fdd8beda583053fe8bf1a2cc8a5 epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 flag-o-matic dc34234e8c43343da45853da22dcf14b libtool f143db5a74ccd9ca28c1234deffede96 ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 1d91b03d42ab6308b5f4f6b598ed110e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=052915aa60b919df12c7c4274d5be551 diff --git a/metadata/md5-cache/sci-biology/embassy-signature-0.1.660 b/metadata/md5-cache/sci-biology/embassy-signature-0.1.660 new file mode 100644 index 000000000000..9f1a9f6f0668 --- /dev/null +++ b/metadata/md5-cache/sci-biology/embassy-signature-0.1.660 @@ -0,0 +1,13 @@ +DEFINED_PHASES=configure install prepare +DEPEND=>=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( dev-db/mysql-connector-c:0= ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] +DESCRIPTION=EMBOSS integrated version of Protein signature add-on package +EAPI=6 +HOMEPAGE=http://emboss.sourceforge.net/ +IUSE=mysql pdf png postgres static-libs X +KEYWORDS=~amd64 ~x86 ~x86-linux +LICENSE=LGPL-2 GPL-2 +RDEPEND=dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( dev-db/mysql-connector-c:0= ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] +SLOT=0 +SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/SIGNATURE-0.1.660.tar.gz -> embassy-signature-0.1.660.tar.gz +_eclasses_=autotools ea7865c8fba1ea8d3639f355fffe1a3c desktop b1d22ac8bdd4679ab79c71aca235009d emboss-r2 4cc77fdd8beda583053fe8bf1a2cc8a5 epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 flag-o-matic dc34234e8c43343da45853da22dcf14b libtool f143db5a74ccd9ca28c1234deffede96 ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 1d91b03d42ab6308b5f4f6b598ed110e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=4cb685046b5a39b624eb3467b815c2c4 diff --git a/metadata/md5-cache/sci-biology/embassy-structure-0.1.660 b/metadata/md5-cache/sci-biology/embassy-structure-0.1.660 new file mode 100644 index 000000000000..45132f23aec2 --- /dev/null +++ b/metadata/md5-cache/sci-biology/embassy-structure-0.1.660 @@ -0,0 +1,13 @@ +DEFINED_PHASES=configure install prepare +DEPEND=>=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( dev-db/mysql-connector-c:0= ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] +DESCRIPTION=EMBOSS integrated version of Protein structure add-on package +EAPI=6 +HOMEPAGE=http://emboss.sourceforge.net/ +IUSE=mysql pdf png postgres static-libs X +KEYWORDS=~amd64 ~x86 ~x86-linux +LICENSE=LGPL-2 GPL-2 +RDEPEND=dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( dev-db/mysql-connector-c:0= ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] +SLOT=0 +SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/STRUCTURE-0.1.660.tar.gz -> embassy-structure-0.1.660.tar.gz +_eclasses_=autotools ea7865c8fba1ea8d3639f355fffe1a3c desktop b1d22ac8bdd4679ab79c71aca235009d emboss-r2 4cc77fdd8beda583053fe8bf1a2cc8a5 epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 flag-o-matic dc34234e8c43343da45853da22dcf14b libtool f143db5a74ccd9ca28c1234deffede96 ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 1d91b03d42ab6308b5f4f6b598ed110e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=634d624be78f958ed7fca02e7dc43bd4 diff --git a/metadata/md5-cache/sci-biology/embassy-topo-2.0.660 b/metadata/md5-cache/sci-biology/embassy-topo-2.0.660 new file mode 100644 index 000000000000..586935e99ad2 --- /dev/null +++ b/metadata/md5-cache/sci-biology/embassy-topo-2.0.660 @@ -0,0 +1,13 @@ +DEFINED_PHASES=configure install prepare +DEPEND=>=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( dev-db/mysql-connector-c:0= ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] +DESCRIPTION=EMBOSS integrated version of Transmembrane protein display +EAPI=6 +HOMEPAGE=http://emboss.sourceforge.net/ +IUSE=mysql pdf png postgres static-libs X +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux +LICENSE=LGPL-2 GPL-2 +RDEPEND=dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( dev-db/mysql-connector-c:0= ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] +SLOT=0 +SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/TOPO-2.0.660.tar.gz -> embassy-topo-2.0.660.tar.gz +_eclasses_=autotools ea7865c8fba1ea8d3639f355fffe1a3c desktop b1d22ac8bdd4679ab79c71aca235009d emboss-r2 4cc77fdd8beda583053fe8bf1a2cc8a5 epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 flag-o-matic dc34234e8c43343da45853da22dcf14b libtool f143db5a74ccd9ca28c1234deffede96 ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 1d91b03d42ab6308b5f4f6b598ed110e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=e50220ee11093554b589c1f9f53e7c09 diff --git a/metadata/md5-cache/sci-biology/embassy-vienna-1.7.2.660 b/metadata/md5-cache/sci-biology/embassy-vienna-1.7.2.660 new file mode 100644 index 000000000000..9a7bbb924403 --- /dev/null +++ b/metadata/md5-cache/sci-biology/embassy-vienna-1.7.2.660 @@ -0,0 +1,13 @@ +DEFINED_PHASES=configure install prepare +DEPEND=>=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( dev-db/mysql-connector-c:0= ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] +DESCRIPTION=EMBOSS integrated version of Vienna RNA package - RNA folding +EAPI=6 +HOMEPAGE=http://emboss.sourceforge.net/ +IUSE=mysql pdf png postgres static-libs X +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux +LICENSE=LGPL-2 GPL-2 +RDEPEND=dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( dev-db/mysql-connector-c:0= ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] +SLOT=0 +SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/VIENNA-1.7.2.660.tar.gz -> embassy-vienna-1.7.2.660.tar.gz +_eclasses_=autotools ea7865c8fba1ea8d3639f355fffe1a3c desktop b1d22ac8bdd4679ab79c71aca235009d emboss-r2 4cc77fdd8beda583053fe8bf1a2cc8a5 epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 flag-o-matic dc34234e8c43343da45853da22dcf14b libtool f143db5a74ccd9ca28c1234deffede96 ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 1d91b03d42ab6308b5f4f6b598ed110e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=d257de40bcdb33c0735daac8a5f15fda diff --git a/metadata/md5-cache/sci-biology/emboss-6.6.0-r1 b/metadata/md5-cache/sci-biology/emboss-6.6.0-r1 new file mode 100644 index 000000000000..19cff0dc635b --- /dev/null +++ b/metadata/md5-cache/sci-biology/emboss-6.6.0-r1 @@ -0,0 +1,14 @@ +DEFINED_PHASES=configure install postinst prepare +DEPEND=>=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( dev-db/mysql-connector-c:0= ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) +DESCRIPTION=The European Molecular Biology Open Software Suite - A sequence analysis package +EAPI=6 +HOMEPAGE=http://emboss.sourceforge.net/ +IUSE=minimal mysql pdf png postgres static-libs X +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux +LICENSE=LGPL-2 GPL-2 Apache-2.0 GPL-3+ CC-BY-3.0 +PDEPEND=!minimal? ( sci-biology/aaindex sci-biology/cutg sci-biology/primer3 sci-biology/prints sci-biology/prosite sci-biology/rebase ) +RDEPEND=!games-action/xbomber !sys-devel/cons dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( dev-db/mysql-connector-c:0= ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? 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( virtual/mpi sys-cluster/mpe2 ) +SLOT=0 +SRC_URI=mirror://gentoo/gibbs-3.1.tar.gz +_eclasses_=autotools ea7865c8fba1ea8d3639f355fffe1a3c libtool f143db5a74ccd9ca28c1234deffede96 multilib 1d91b03d42ab6308b5f4f6b598ed110e toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c +_md5_=8d48efee68d1063803fccbc4c73a0f5d diff --git a/metadata/md5-cache/sci-biology/glimmer-3.02-r3 b/metadata/md5-cache/sci-biology/glimmer-3.02-r3 new file mode 100644 index 000000000000..05ddf3e08914 --- /dev/null +++ b/metadata/md5-cache/sci-biology/glimmer-3.02-r3 @@ -0,0 +1,11 @@ +DEFINED_PHASES=compile install prepare +DESCRIPTION=An HMM-based microbial gene finding system from TIGR +EAPI=5 +HOMEPAGE=https://ccb.jhu.edu/software/glimmer/index.shtml +KEYWORDS=amd64 x86 +LICENSE=Artistic +RDEPEND=app-shells/tcsh +SLOT=0 +SRC_URI=http://www.cbcb.umd.edu/software/glimmer/glimmer302.tar.gz +_eclasses_=desktop b1d22ac8bdd4679ab79c71aca235009d epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 1d91b03d42ab6308b5f4f6b598ed110e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=94600a4de5a2dc02bc6652d958a2a034 diff --git a/metadata/md5-cache/sci-biology/glimmer-3.02b b/metadata/md5-cache/sci-biology/glimmer-3.02b new file mode 100644 index 000000000000..184cc8f028c5 --- /dev/null +++ b/metadata/md5-cache/sci-biology/glimmer-3.02b @@ -0,0 +1,11 @@ +DEFINED_PHASES=compile install prepare +DESCRIPTION=An HMM-based microbial gene finding system from TIGR +EAPI=5 +HOMEPAGE=https://ccb.jhu.edu/software/glimmer/index.shtml +KEYWORDS=~amd64 ~x86 +LICENSE=Artistic +RDEPEND=app-shells/tcsh sci-biology/elph +SLOT=0 +SRC_URI=https://ccb.jhu.edu/software/glimmer/glimmer302b.tar.gz +_eclasses_=desktop b1d22ac8bdd4679ab79c71aca235009d epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 1d91b03d42ab6308b5f4f6b598ed110e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=6916d92c69198563f19b744f1e57dddc diff --git a/metadata/md5-cache/sci-biology/glimmerhmm-3.0.1-r1 b/metadata/md5-cache/sci-biology/glimmerhmm-3.0.1-r1 new file mode 100644 index 000000000000..de218b00d488 --- /dev/null +++ b/metadata/md5-cache/sci-biology/glimmerhmm-3.0.1-r1 @@ -0,0 +1,10 @@ +DEFINED_PHASES=compile configure install +DESCRIPTION=A eukaryotic gene finding system from TIGR +EAPI=7 +HOMEPAGE=http://www.cbcb.umd.edu/software/GlimmerHMM/ +KEYWORDS=amd64 x86 +LICENSE=Artistic +SLOT=0 +SRC_URI=ftp://ftp.cbcb.umd.edu/pub/software/glimmerhmm/GlimmerHMM-3.0.1.tar.gz +_eclasses_=multilib 1d91b03d42ab6308b5f4f6b598ed110e toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c +_md5_=9fc33629a982f35b93c18da772894fdd diff --git a/metadata/md5-cache/sci-biology/gmap-2015.12.31.5 b/metadata/md5-cache/sci-biology/gmap-2015.12.31.5 new file mode 100644 index 000000000000..9af4c172fcc5 --- /dev/null +++ b/metadata/md5-cache/sci-biology/gmap-2015.12.31.5 @@ -0,0 +1,10 @@ +DEFINED_PHASES=- +DESCRIPTION=A Genomic Mapping and Alignment Program for mRNA and EST Sequences +EAPI=6 +HOMEPAGE=http://research-pub.gene.com/gmap/ +KEYWORDS=~amd64 ~x86 +LICENSE=gmap +SLOT=0 +SRC_URI=http://research-pub.gene.com/gmap/src/gmap-gsnap-2015-12-31.v5.tar.gz +_eclasses_=estack 686eaab303305a908fd57b2fd7617800 versionator 2352c3fc97241f6a02042773c8287748 +_md5_=398e7f0670f5bd07e45f2780d7fe03cf diff --git a/metadata/md5-cache/sci-biology/hmmer-2.3.2-r4 b/metadata/md5-cache/sci-biology/hmmer-2.3.2-r4 new file mode 100644 index 000000000000..9bc345ffd85e --- /dev/null +++ b/metadata/md5-cache/sci-biology/hmmer-2.3.2-r4 @@ -0,0 +1,12 @@ +DEFINED_PHASES=configure install postinst +DEPEND=test? ( dev-lang/perl ) +DESCRIPTION=Sequence analysis using profile hidden Markov models +EAPI=6 +HOMEPAGE=http://hmmer.org/ +IUSE=altivec test threads +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-2 +RESTRICT=!test? ( test ) +SLOT=2 +SRC_URI=http://eddylab.org/software/hmmer/2.3.2/hmmer-2.3.2.tar.gz +_md5_=e7199c0c0fe31d6c32ec1e285d23d2c8 diff --git a/metadata/md5-cache/sci-biology/hmmer-3.1_beta2 b/metadata/md5-cache/sci-biology/hmmer-3.1_beta2 new file mode 100644 index 000000000000..0dfc8524d7bb --- /dev/null +++ b/metadata/md5-cache/sci-biology/hmmer-3.1_beta2 @@ -0,0 +1,13 @@ +DEFINED_PHASES=configure install +DEPEND=mpi? ( virtual/mpi ) gsl? ( sci-libs/gsl:= ) test? ( dev-lang/perl ) +DESCRIPTION=Sequence analysis using profile hidden Markov models +EAPI=6 +HOMEPAGE=http://hmmer.org/ +IUSE=altivec cpu_flags_x86_sse gsl mpi test +threads +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos +LICENSE=GPL-3 +RDEPEND=mpi? ( virtual/mpi ) gsl? ( sci-libs/gsl:= ) +RESTRICT=!test? ( test ) +SLOT=0 +SRC_URI=http://eddylab.org/software/hmmer3/3.1b2/hmmer-3.1b2.tar.gz +_md5_=96e45fe8b653c57b833ec948674bbe69 diff --git a/metadata/md5-cache/sci-biology/iedera-1.05-r1 b/metadata/md5-cache/sci-biology/iedera-1.05-r1 new file mode 100644 index 000000000000..2434f1a12e2f --- /dev/null +++ b/metadata/md5-cache/sci-biology/iedera-1.05-r1 @@ -0,0 +1,11 @@ +DEFINED_PHASES=prepare +DEPEND=>=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 +DESCRIPTION=A subset seed design tool for DNA sequence alignment +EAPI=6 +HOMEPAGE=http://bioinfo.lifl.fr/yass/iedera.php +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-2 +SLOT=0 +SRC_URI=http://bioinfo.lifl.fr/yass/files/iedera-1.05.tar.gz +_eclasses_=autotools ea7865c8fba1ea8d3639f355fffe1a3c libtool f143db5a74ccd9ca28c1234deffede96 multilib 1d91b03d42ab6308b5f4f6b598ed110e toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c +_md5_=ce77e1e27bd52fed2fd2af52744d6288 diff --git a/metadata/md5-cache/sci-biology/infernal-1.0.2-r1 b/metadata/md5-cache/sci-biology/infernal-1.0.2-r1 new file mode 100644 index 000000000000..e3d478338308 --- /dev/null +++ b/metadata/md5-cache/sci-biology/infernal-1.0.2-r1 @@ -0,0 +1,12 @@ +DEFINED_PHASES=configure install +DEPEND=mpi? ( virtual/mpi ) +DESCRIPTION=Inference of RNA alignments +EAPI=6 +HOMEPAGE=http://infernal.janelia.org/ +IUSE=mpi +KEYWORDS=amd64 x86 +LICENSE=GPL-3 +RDEPEND=mpi? ( virtual/mpi ) +SLOT=0 +SRC_URI=ftp://selab.janelia.org/pub/software/infernal/infernal-1.0.2.tar.gz +_md5_=a3cee86cfd4ecbef4e39563bc652a64b diff --git a/metadata/md5-cache/sci-biology/iqpnni-3.3.2-r1 b/metadata/md5-cache/sci-biology/iqpnni-3.3.2-r1 new file mode 100644 index 000000000000..975248a39250 --- /dev/null +++ b/metadata/md5-cache/sci-biology/iqpnni-3.3.2-r1 @@ -0,0 +1,10 @@ +DEFINED_PHASES=install +DESCRIPTION=Important Quartet Puzzling and NNI Operation +EAPI=6 +HOMEPAGE=http://www.cibiv.at/software/iqpnni/ +IUSE=doc +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-2 +SLOT=0 +SRC_URI=http://www.cibiv.at/software/iqpnni/iqpnni-3.3.2.tar.gz +_md5_=871193b79341fc00590227fc8ec7d4d4 diff --git a/metadata/md5-cache/sci-biology/kalign-2.03-r2 b/metadata/md5-cache/sci-biology/kalign-2.03-r2 new file mode 100644 index 000000000000..a5fcb613d3bf --- /dev/null +++ b/metadata/md5-cache/sci-biology/kalign-2.03-r2 @@ -0,0 +1,10 @@ +DEFINED_PHASES=compile install prepare +DESCRIPTION=Global and progressive multiple sequence alignment +EAPI=6 +HOMEPAGE=http://msa.cgb.ki.se/ +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-2 +SLOT=0 +SRC_URI=mirror://debian/pool/main/k/kalign/kalign_2.03.orig.tar.gz +_eclasses_=multilib 1d91b03d42ab6308b5f4f6b598ed110e toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c +_md5_=175d26382226c7bed2b44be485b01d01 diff --git a/metadata/md5-cache/sci-biology/kallisto-0.43.1 b/metadata/md5-cache/sci-biology/kallisto-0.43.1 new file mode 100644 index 000000000000..ef8dec5c38bf --- /dev/null +++ b/metadata/md5-cache/sci-biology/kallisto-0.43.1 @@ -0,0 +1,12 @@ +DEFINED_PHASES=compile configure install prepare test +DEPEND=sci-libs/hdf5:= sys-libs/zlib:= sys-devel/make >=dev-util/cmake-3.9.6 +DESCRIPTION=Near-optimal RNA-Seq quantification +EAPI=6 +HOMEPAGE=http://pachterlab.github.io/kallisto/ +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux +LICENSE=BSD +RDEPEND=sci-libs/hdf5:= sys-libs/zlib:= +SLOT=0 +SRC_URI=https://github.com/pachterlab/kallisto/archive/v0.43.1.tar.gz -> kallisto-0.43.1.tar.gz +_eclasses_=cmake-utils be72eac95bd029ad1d81d5d656c3c83b desktop b1d22ac8bdd4679ab79c71aca235009d epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 flag-o-matic dc34234e8c43343da45853da22dcf14b ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 1d91b03d42ab6308b5f4f6b598ed110e multiprocessing cac3169468f893670dac3e7cb940e045 ninja-utils 132cbb376048d079b5a012f5467c4e7f preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf xdg-utils ff2ff954e6b17929574eee4efc5152ba +_md5_=b5fc562bf49e70db44b86bc5702ae9f2 diff --git a/metadata/md5-cache/sci-biology/kallisto-9999 b/metadata/md5-cache/sci-biology/kallisto-9999 new file mode 100644 index 000000000000..1f6b714faef6 --- /dev/null +++ b/metadata/md5-cache/sci-biology/kallisto-9999 @@ -0,0 +1,11 @@ +DEFINED_PHASES=compile configure install prepare test unpack 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+DESCRIPTION=Genome-scale comparison of biological sequences +EAPI=6 +HOMEPAGE=http://last.cbrc.jp/ +IUSE=+python_targets_python2_7 +python_single_target_python2_7 +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-3 +RDEPEND=python_single_target_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 >=dev-lang/python-exec-2:=[python_targets_python2_7] ) +REQUIRED_USE=^^ ( python_single_target_python2_7 ) python_single_target_python2_7? ( python_targets_python2_7 ) +SLOT=0 +SRC_URI=http://last.cbrc.jp/last-299.zip +_eclasses_=multilib 1d91b03d42ab6308b5f4f6b598ed110e python-single-r1 36ac48e647d2627de28c87aaffb94753 python-utils-r1 611c493a4cfef5254350fabc04b606f5 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c +_md5_=ec5206661373a6ef6ad77450dfbdb915 diff --git a/metadata/md5-cache/sci-biology/libgtextutils-0.6.1 b/metadata/md5-cache/sci-biology/libgtextutils-0.6.1 new file mode 100644 index 000000000000..e08da53b29df --- /dev/null +++ b/metadata/md5-cache/sci-biology/libgtextutils-0.6.1 @@ -0,0 +1,11 @@ +DEFINED_PHASES=configure install prepare +DEPEND=>=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 +DESCRIPTION=Gordon Text utils Library +EAPI=6 +HOMEPAGE=http://hannonlab.cshl.edu/fastx_toolkit/ +KEYWORDS=~amd64 ~x86 +LICENSE=AGPL-3 +SLOT=0/0 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+SRC_URI=https://mafft.cbrc.jp/alignment/software/mafft-7.215-without-extensions-src.tgz +_eclasses_=desktop b1d22ac8bdd4679ab79c71aca235009d epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 flag-o-matic dc34234e8c43343da45853da22dcf14b ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 1d91b03d42ab6308b5f4f6b598ed110e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=7b8b136195c000efff0407f671d57f19 diff --git a/metadata/md5-cache/sci-biology/mafft-7.305 b/metadata/md5-cache/sci-biology/mafft-7.305 new file mode 100644 index 000000000000..413035cf467d --- /dev/null +++ b/metadata/md5-cache/sci-biology/mafft-7.305 @@ -0,0 +1,11 @@ +DEFINED_PHASES=compile install prepare test +DESCRIPTION=Multiple sequence alignments using a variety of algorithms +EAPI=6 +HOMEPAGE=https://mafft.cbrc.jp/alignment/software/index.html +IUSE=threads +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos +LICENSE=BSD +SLOT=0 +SRC_URI=https://mafft.cbrc.jp/alignment/software/mafft-7.305-without-extensions-src.tgz +_eclasses_=desktop b1d22ac8bdd4679ab79c71aca235009d epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 flag-o-matic dc34234e8c43343da45853da22dcf14b ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 1d91b03d42ab6308b5f4f6b598ed110e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=920a37021a0b392bb7315b63cf3de39d diff --git a/metadata/md5-cache/sci-biology/maq-0.7.1-r2 b/metadata/md5-cache/sci-biology/maq-0.7.1-r2 new file mode 100644 index 000000000000..c324a5f7f198 --- /dev/null +++ b/metadata/md5-cache/sci-biology/maq-0.7.1-r2 @@ -0,0 +1,12 @@ +DEFINED_PHASES=install prepare +DEPEND=sys-libs/zlib >=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 +DESCRIPTION=Mapping and Assembly with Qualities, mapping NGS reads to reference genomes +EAPI=6 +HOMEPAGE=http://maq.sourceforge.net/ +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux +LICENSE=GPL-3 +RDEPEND=sys-libs/zlib +SLOT=0 +SRC_URI=mirror://sourceforge/maq/maq-0.7.1.tar.bz2 mirror://sourceforge/maq/calib-36.dat.gz +_eclasses_=autotools ea7865c8fba1ea8d3639f355fffe1a3c libtool f143db5a74ccd9ca28c1234deffede96 multilib 1d91b03d42ab6308b5f4f6b598ed110e toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c +_md5_=39ffb0025210075a8d7d7f6f81f8da56 diff --git a/metadata/md5-cache/sci-biology/maqview-0.2.5-r3 b/metadata/md5-cache/sci-biology/maqview-0.2.5-r3 new file mode 100644 index 000000000000..85bee8243c0d --- /dev/null +++ b/metadata/md5-cache/sci-biology/maqview-0.2.5-r3 @@ -0,0 +1,12 @@ +DEFINED_PHASES=prepare +DEPEND=media-libs/freeglut sys-libs/zlib >=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 +DESCRIPTION=GUI for sci-biology/maq, a short read mapping assembler +EAPI=6 +HOMEPAGE=http://maq.sourceforge.net/ +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-3 +RDEPEND=media-libs/freeglut sys-libs/zlib sci-biology/maq +SLOT=0 +SRC_URI=mirror://sourceforge/maq/maqview-0.2.5.tar.gz +_eclasses_=autotools ea7865c8fba1ea8d3639f355fffe1a3c libtool f143db5a74ccd9ca28c1234deffede96 multilib 1d91b03d42ab6308b5f4f6b598ed110e toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c +_md5_=dee50558d10e75ff9e96f4c3f177c55f diff --git a/metadata/md5-cache/sci-biology/mcl-14.137 b/metadata/md5-cache/sci-biology/mcl-14.137 new file mode 100644 index 000000000000..cbc05276454e --- /dev/null +++ b/metadata/md5-cache/sci-biology/mcl-14.137 @@ -0,0 +1,12 @@ +DEFINED_PHASES=configure prepare +DEPEND=>=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 +DESCRIPTION=A Markov Cluster Algorithm implementation +EAPI=6 +HOMEPAGE=http://micans.org/mcl/ +IUSE=+blast +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-2 +SLOT=0 +SRC_URI=http://micans.org/mcl/src/mcl-14-137.tar.gz +_eclasses_=autotools ea7865c8fba1ea8d3639f355fffe1a3c libtool f143db5a74ccd9ca28c1234deffede96 multilib 1d91b03d42ab6308b5f4f6b598ed110e toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c +_md5_=3429c68609b6c70e047d577379f68f97 diff --git a/metadata/md5-cache/sci-biology/meme-4.11.2_p2 b/metadata/md5-cache/sci-biology/meme-4.11.2_p2 new file mode 100644 index 000000000000..edb91025ba4b --- /dev/null +++ b/metadata/md5-cache/sci-biology/meme-4.11.2_p2 @@ -0,0 +1,14 @@ +DEFINED_PHASES=configure install prepare setup test +DEPEND=python_single_target_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 >=dev-lang/python-exec-2:=[python_targets_python2_7] ) app-shells/tcsh dev-libs/libxml2:2 dev-libs/libxslt sys-libs/zlib app-text/ghostscript-gpl media-gfx/imagemagick dev-lang/perl:= dev-perl/HTML-Parser dev-perl/HTML-Template dev-perl/Log-Log4perl dev-perl/Math-CDF dev-perl/XML-Compile-SOAP dev-perl/XML-Compile-WSDL11 dev-perl/XML-Parser dev-perl/XML-Simple virtual/perl-Data-Dumper virtual/perl-Exporter virtual/perl-File-Path virtual/perl-File-Spec virtual/perl-File-Temp virtual/perl-Getopt-Long virtual/perl-Scalar-List-Utils virtual/perl-Time-HiRes mpi? ( virtual/mpi ) >=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 +DESCRIPTION=The MEME/MAST system - Motif discovery and search +EAPI=6 +HOMEPAGE=http://meme-suite.org/tools/meme +IUSE=debug doc examples mpi +python_targets_python2_7 +python_single_target_python2_7 +KEYWORDS=~amd64 ~x86 +LICENSE=meme +RDEPEND=python_single_target_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 >=dev-lang/python-exec-2:=[python_targets_python2_7] ) app-shells/tcsh dev-libs/libxml2:2 dev-libs/libxslt sys-libs/zlib app-text/ghostscript-gpl media-gfx/imagemagick dev-lang/perl:= dev-perl/HTML-Parser dev-perl/HTML-Template dev-perl/Log-Log4perl dev-perl/Math-CDF dev-perl/XML-Compile-SOAP dev-perl/XML-Compile-WSDL11 dev-perl/XML-Parser dev-perl/XML-Simple virtual/perl-Data-Dumper virtual/perl-Exporter virtual/perl-File-Path virtual/perl-File-Spec virtual/perl-File-Temp virtual/perl-Getopt-Long virtual/perl-Scalar-List-Utils virtual/perl-Time-HiRes mpi? ( virtual/mpi ) +REQUIRED_USE=^^ ( python_single_target_python2_7 ) python_single_target_python2_7? ( python_targets_python2_7 ) +SLOT=0 +SRC_URI=http://meme-suite.org/meme-software/4.11.2/meme_4.11.2.tar.gz +_eclasses_=autotools ea7865c8fba1ea8d3639f355fffe1a3c estack 686eaab303305a908fd57b2fd7617800 libtool f143db5a74ccd9ca28c1234deffede96 multilib 1d91b03d42ab6308b5f4f6b598ed110e perl-functions 6ec4c4d8fc8324200f1c14e8d158c59b python-single-r1 36ac48e647d2627de28c87aaffb94753 python-utils-r1 611c493a4cfef5254350fabc04b606f5 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c versionator 2352c3fc97241f6a02042773c8287748 +_md5_=a4080439675628436c06de8db9f59c6e diff --git a/metadata/md5-cache/sci-biology/mira-4.0.2 b/metadata/md5-cache/sci-biology/mira-4.0.2 new file mode 100644 index 000000000000..7621fb5438e4 --- /dev/null +++ b/metadata/md5-cache/sci-biology/mira-4.0.2 @@ -0,0 +1,13 @@ +DEFINED_PHASES=configure install postinst prepare +DEPEND=dev-libs/boost[threads] dev-util/google-perftools sys-devel/flex app-editors/vim-core dev-libs/expat >=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 +DESCRIPTION=Whole Genome Shotgun and EST Sequence Assembler for Sanger, 454 and Illumina +EAPI=6 +HOMEPAGE=http://www.chevreux.org/projects_mira.html +IUSE=doc +KEYWORDS=amd64 x86 ~amd64-linux ~x86-linux ~x86-macos +LICENSE=GPL-2 +RDEPEND=dev-libs/boost[threads] dev-util/google-perftools +SLOT=0 +SRC_URI=https://sourceforge.net/projects/mira-assembler/files/MIRA/stable/mira-4.0.2.tar.bz2 mirror://sourceforge/mira-assembler/mira_3rdparty_06-07-2012.tar.bz2 +_eclasses_=autotools ea7865c8fba1ea8d3639f355fffe1a3c desktop b1d22ac8bdd4679ab79c71aca235009d epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 libtool f143db5a74ccd9ca28c1234deffede96 ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 1d91b03d42ab6308b5f4f6b598ed110e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=e7b4c654f7c0055be7ef6347b5bdfb8a diff --git a/metadata/md5-cache/sci-biology/mosaik-2.2.30 b/metadata/md5-cache/sci-biology/mosaik-2.2.30 new file mode 100644 index 000000000000..aee6c614a1d8 --- /dev/null +++ b/metadata/md5-cache/sci-biology/mosaik-2.2.30 @@ -0,0 +1,10 @@ +DEFINED_PHASES=compile configure install unpack +DESCRIPTION=A reference-guided aligner for next-generation sequencing technologies +EAPI=6 +HOMEPAGE=https://github.com/wanpinglee/MOSAIK +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-2 +SLOT=0 +SRC_URI=https://github.com/wanpinglee/MOSAIK/archive/5c25216d3522d6a33e53875cd76a6d65001e4e67.tar.gz -> mosaik-2.2.30.tar.gz +_eclasses_=desktop b1d22ac8bdd4679ab79c71aca235009d epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 flag-o-matic dc34234e8c43343da45853da22dcf14b ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 1d91b03d42ab6308b5f4f6b598ed110e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf vcs-snapshot b1abf460a493fc59ebb25de0df3f09dd +_md5_=630686b35f8a549c580c5fd0e2cb02fc diff --git a/metadata/md5-cache/sci-biology/mothur-1.27.0-r1 b/metadata/md5-cache/sci-biology/mothur-1.27.0-r1 new file mode 100644 index 000000000000..8c62d6800dec --- /dev/null +++ b/metadata/md5-cache/sci-biology/mothur-1.27.0-r1 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile install prepare setup +DEPEND=sci-biology/uchime mpi? ( virtual/mpi ) app-arch/unzip virtual/fortran +DESCRIPTION=A suite of algorithms for ecological bioinformatics +EAPI=5 +HOMEPAGE=https://www.mothur.org/ +IUSE=mpi +readline +KEYWORDS=amd64 x86 +LICENSE=GPL-3 +RDEPEND=sci-biology/uchime mpi? ( virtual/mpi ) virtual/fortran +SLOT=0 +SRC_URI=https://www.mothur.org/w/images/c/cb/Mothur.1.27.0.zip -> mothur-1.27.0.zip +_eclasses_=desktop b1d22ac8bdd4679ab79c71aca235009d epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 flag-o-matic dc34234e8c43343da45853da22dcf14b fortran-2 216ce6fa0e81c0c91667aee598c792dd ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 1d91b03d42ab6308b5f4f6b598ed110e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=17f8b3c73710bbb746fc4cbfcf78b85d diff --git a/metadata/md5-cache/sci-biology/mrbayes-3.1.2-r2 b/metadata/md5-cache/sci-biology/mrbayes-3.1.2-r2 new file mode 100644 index 000000000000..9caa1de71d7a --- /dev/null +++ b/metadata/md5-cache/sci-biology/mrbayes-3.1.2-r2 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile install prepare +DEPEND=sys-libs/ncurses:0= mpi? ( virtual/mpi ) readline? ( sys-libs/readline:0= ) +DESCRIPTION=Bayesian Inference of Phylogeny +EAPI=5 +HOMEPAGE=http://mrbayes.csit.fsu.edu/ +IUSE=debug mpi readline +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris +LICENSE=GPL-2 +RDEPEND=sys-libs/ncurses:0= mpi? ( virtual/mpi ) readline? ( sys-libs/readline:0= ) +SLOT=0 +SRC_URI=mirror://sourceforge/mrbayes/mrbayes-3.1.2.tar.gz +_eclasses_=desktop b1d22ac8bdd4679ab79c71aca235009d epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 1d91b03d42ab6308b5f4f6b598ed110e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=a944448f568e57bb9f221cd1f437ab09 diff --git a/metadata/md5-cache/sci-biology/mummer-3.23 b/metadata/md5-cache/sci-biology/mummer-3.23 new file mode 100644 index 000000000000..8b081da45274 --- /dev/null +++ b/metadata/md5-cache/sci-biology/mummer-3.23 @@ -0,0 +1,12 @@ +DEFINED_PHASES=configure install +DESCRIPTION=A rapid whole genome aligner +EAPI=6 +HOMEPAGE=http://mummer.sourceforge.net/ +IUSE=doc +KEYWORDS=~amd64 ~x86 +LICENSE=Artistic +RDEPEND=app-shells/tcsh dev-lang/perl +SLOT=0 +SRC_URI=mirror://sourceforge/mummer/MUMmer3.23.tar.gz +_eclasses_=desktop b1d22ac8bdd4679ab79c71aca235009d epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 flag-o-matic dc34234e8c43343da45853da22dcf14b ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 1d91b03d42ab6308b5f4f6b598ed110e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=c256f298b416306c1be7005e7877f7b9 diff --git a/metadata/md5-cache/sci-biology/muscle-3.8.31 b/metadata/md5-cache/sci-biology/muscle-3.8.31 new file mode 100644 index 000000000000..b4c1f09a187a --- /dev/null +++ b/metadata/md5-cache/sci-biology/muscle-3.8.31 @@ -0,0 +1,11 @@ +DEFINED_PHASES=install prepare +DESCRIPTION=Multiple sequence comparison by log-expectation +EAPI=5 +HOMEPAGE=http://www.drive5.com/muscle/ +KEYWORDS=amd64 ppc x86 +LICENSE=public-domain +RDEPEND=!sci-libs/libmuscle +SLOT=0 +SRC_URI=http://www.drive5.com/muscle/downloads3.8.31/muscle3.8.31_src.tar.gz +_eclasses_=desktop b1d22ac8bdd4679ab79c71aca235009d epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 1d91b03d42ab6308b5f4f6b598ed110e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=500ff424aff8c56744362bc87a3ff285 diff --git a/metadata/md5-cache/sci-biology/ncbi-tools-2.2.26-r2 b/metadata/md5-cache/sci-biology/ncbi-tools-2.2.26-r2 new file mode 100644 index 000000000000..84e5be0d0bd2 --- /dev/null +++ b/metadata/md5-cache/sci-biology/ncbi-tools-2.2.26-r2 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile install prepare setup +DEPEND=app-shells/tcsh dev-lang/perl media-libs/libpng:0= X? ( media-libs/fontconfig x11-libs/motif:0= x11-libs/libICE x11-libs/libX11 x11-libs/libXft x11-libs/libXmu x11-libs/libXt ) +DESCRIPTION=Development toolkit and applications for computational biology, including BLAST +EAPI=5 +HOMEPAGE=https://www.ncbi.nlm.nih.gov/ +IUSE=doc static-libs X +KEYWORDS=~alpha amd64 ppc64 x86 ~amd64-linux ~x86-linux ~ppc-macos +LICENSE=public-domain +RDEPEND=app-shells/tcsh dev-lang/perl media-libs/libpng:0= X? ( media-libs/fontconfig x11-libs/motif:0= x11-libs/libICE x11-libs/libX11 x11-libs/libXft x11-libs/libXmu x11-libs/libXt ) +SLOT=0 +SRC_URI=ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/2.2.26/ncbi.tar.gz -> ncbi-tools-2.2.26.tar.gz +_eclasses_=desktop b1d22ac8bdd4679ab79c71aca235009d epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 flag-o-matic dc34234e8c43343da45853da22dcf14b ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 1d91b03d42ab6308b5f4f6b598ed110e prefix c2993e4c430c1ee24f278983d6189501 preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=8bcc533f96e3c3fe8bf6e5b090a4dacd diff --git a/metadata/md5-cache/sci-biology/newick-utils-1.6 b/metadata/md5-cache/sci-biology/newick-utils-1.6 new file mode 100644 index 000000000000..f9cdb1fd46cd --- /dev/null +++ b/metadata/md5-cache/sci-biology/newick-utils-1.6 @@ -0,0 +1,10 @@ +DEFINED_PHASES=test +DESCRIPTION=Tools for processing phylogenetic trees +EAPI=6 +HOMEPAGE=http://cegg.unige.ch/newick_utils +KEYWORDS=~amd64 ~x86 +LICENSE=BSD +RDEPEND=!dev-games/libnw +SLOT=0 +SRC_URI=http://cegg.unige.ch/pub/newick-utils-1.6.tar.gz +_md5_=f70356a582d317400bf4cd17b73beb16 diff --git a/metadata/md5-cache/sci-biology/njplot-2.3-r2 b/metadata/md5-cache/sci-biology/njplot-2.3-r2 new file mode 100644 index 000000000000..5a4a9d6c18b2 --- /dev/null +++ b/metadata/md5-cache/sci-biology/njplot-2.3-r2 @@ -0,0 +1,12 @@ +DEFINED_PHASES=install prepare +DEPEND=sci-biology/ncbi-tools[X,static-libs] x11-libs/libXmu +DESCRIPTION=A phylogenetic tree drawing program which supports tree rooting +EAPI=6 +HOMEPAGE=http://pbil.univ-lyon1.fr/software/njplot.html +KEYWORDS=~amd64 ~x86 +LICENSE=public-domain +RDEPEND=sci-biology/ncbi-tools[X,static-libs] x11-libs/libXmu +SLOT=0 +SRC_URI=ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/njplot/archive/njplot-2.3.tar.gz +_eclasses_=multilib 1d91b03d42ab6308b5f4f6b598ed110e toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c +_md5_=c70b49c7f5e1a92f5169df372f9638c6 diff --git a/metadata/md5-cache/sci-biology/pals-1.0-r1 b/metadata/md5-cache/sci-biology/pals-1.0-r1 new file mode 100644 index 000000000000..7985e93e73dc --- /dev/null +++ b/metadata/md5-cache/sci-biology/pals-1.0-r1 @@ -0,0 +1,10 @@ +DEFINED_PHASES=configure install +DESCRIPTION=Pairwise Aligner for Long Sequences +EAPI=6 +HOMEPAGE=http://www.drive5.com/pals/ +KEYWORDS=amd64 x86 +LICENSE=public-domain +SLOT=0 +SRC_URI=http://www.drive5.com/pals/pals_source.tar.gz -> pals-1.0.tar.gz +_eclasses_=multilib 1d91b03d42ab6308b5f4f6b598ed110e toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c +_md5_=b0df20d47905df6a290c5fe2f79fd48b diff --git a/metadata/md5-cache/sci-biology/paml-4.4c-r1 b/metadata/md5-cache/sci-biology/paml-4.4c-r1 new file mode 100644 index 000000000000..acfc7f0e0314 --- /dev/null +++ b/metadata/md5-cache/sci-biology/paml-4.4c-r1 @@ 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+++ b/metadata/md5-cache/sci-biology/phylip-3.69-r1 @@ -0,0 +1,12 @@ +DEFINED_PHASES=compile install prepare +DEPEND=x11-libs/libXaw x11-base/xorg-proto +DESCRIPTION=The PHYLogeny Inference Package +EAPI=5 +HOMEPAGE=http://evolution.genetics.washington.edu/phylip.html +KEYWORDS=amd64 ppc x86 ~amd64-linux ~x86-linux ~ppc-macos +LICENSE=free-noncomm +RDEPEND=x11-libs/libXaw +SLOT=0 +SRC_URI=http://evolution.gs.washington.edu/phylip/download/phylip-3.69.tar.gz +_eclasses_=multilib 1d91b03d42ab6308b5f4f6b598ed110e toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c +_md5_=b42cd8579055d407d2b75b6dccdf2c7a diff --git a/metadata/md5-cache/sci-biology/phylip-3.696-r1 b/metadata/md5-cache/sci-biology/phylip-3.696-r1 new file mode 100644 index 000000000000..8b79f9a93766 --- /dev/null +++ b/metadata/md5-cache/sci-biology/phylip-3.696-r1 @@ -0,0 +1,12 @@ +DEFINED_PHASES=compile install prepare +DEPEND=x11-libs/libXaw x11-base/xorg-proto +DESCRIPTION=The PHYLogeny Inference Package +EAPI=5 +HOMEPAGE=http://evolution.genetics.washington.edu/phylip.html +KEYWORDS=~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos +LICENSE=BSD-2 +RDEPEND=x11-libs/libXaw +SLOT=0 +SRC_URI=http://evolution.gs.washington.edu/phylip/download/phylip-3.696.tar.gz +_eclasses_=multilib 1d91b03d42ab6308b5f4f6b598ed110e toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c +_md5_=0e36eb92b11c05e1704acd5ce863d792 diff --git a/metadata/md5-cache/sci-biology/phylip-3.696-r2 b/metadata/md5-cache/sci-biology/phylip-3.696-r2 new file mode 100644 index 000000000000..f9536fa8961d --- /dev/null +++ b/metadata/md5-cache/sci-biology/phylip-3.696-r2 @@ -0,0 +1,12 @@ +DEFINED_PHASES=compile install prepare +DEPEND=x11-libs/libXaw !!dev-lang/elixir x11-base/xorg-proto +DESCRIPTION=The PHYLogeny Inference Package +EAPI=5 +HOMEPAGE=http://evolution.genetics.washington.edu/phylip.html +KEYWORDS=~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos +LICENSE=BSD-2 +RDEPEND=x11-libs/libXaw !!dev-lang/elixir +SLOT=0 +SRC_URI=http://evolution.gs.washington.edu/phylip/download/phylip-3.696.tar.gz +_eclasses_=multilib 1d91b03d42ab6308b5f4f6b598ed110e toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c +_md5_=33ab1d7ce3016bdb569e9fd1a4fd5d90 diff --git a/metadata/md5-cache/sci-biology/phyml-2.4.5-r3 b/metadata/md5-cache/sci-biology/phyml-2.4.5-r3 new file mode 100644 index 000000000000..40d0bde5f5b7 --- /dev/null +++ b/metadata/md5-cache/sci-biology/phyml-2.4.5-r3 @@ -0,0 +1,10 @@ +DEFINED_PHASES=install prepare +DESCRIPTION=Estimation of large phylogenies by maximum likelihood +EAPI=6 +HOMEPAGE=http://atgc.lirmm.fr/phyml/ +KEYWORDS=amd64 ppc x86 +LICENSE=GPL-2 +SLOT=0 +SRC_URI=http://www.lirmm.fr/~guindon/phyml_v2.4.5.tar.gz +_eclasses_=multilib 1d91b03d42ab6308b5f4f6b598ed110e toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c +_md5_=fcca6fb4f9e88f5eb6a63a3ee0c79df7 diff --git a/metadata/md5-cache/sci-biology/picard-1.103 b/metadata/md5-cache/sci-biology/picard-1.103 new file mode 100644 index 000000000000..e84bf998cd1c --- /dev/null +++ b/metadata/md5-cache/sci-biology/picard-1.103 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile configure install preinst prepare setup test +DEPEND=>=virtual/jdk-1.6 dev-java/ant-apache-bcel:0 test? ( dev-java/testng:0 dev-lang/R ) dev-java/snappy:1.0 dev-java/cofoja:0 dev-java/commons-jexl:2 dev-java/ant-core:0 >=dev-java/java-config-2.2.0-r3 source? ( app-arch/zip ) >=dev-java/ant-core-1.8.2:0 dev-java/ant-apache-bcel dev-java/testng:0 dev-java/ant-junit4 >=dev-java/javatoolkit-0.3.0-r2 +DESCRIPTION=Java-based command-line utilities that manipulate SAM files +EAPI=5 +HOMEPAGE=http://picard.sourceforge.net/ +IUSE=elibc_FreeBSD doc source test elibc_FreeBSD +KEYWORDS=~amd64 ~x86 +LICENSE=Apache-2.0 +RDEPEND=>=virtual/jre-1.6 dev-java/snappy:1.0 dev-java/cofoja:0 dev-java/commons-jexl:2 dev-java/ant-core:0 >=dev-java/java-config-2.2.0-r3 source? ( app-arch/zip ) +RESTRICT=!test? ( test ) !test? ( test ) +SLOT=0 +SRC_URI=https://dev.gentoo.org/~ercpe/distfiles/sci-biology/picard/picard-1.103.tar.bz2 +_eclasses_=desktop b1d22ac8bdd4679ab79c71aca235009d eapi7-ver 756b3f27d8e46131d5cf3c51bd876446 epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 java-ant-2 8d9cb415f1ca9fc7ebc5a74bacec300c java-pkg-2 c4e6af2574fd1dc79b43a6e27af4b5fb java-utils-2 a055407af6fd37cf3f692ba73d2d2ba5 ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 1d91b03d42ab6308b5f4f6b598ed110e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf versionator 2352c3fc97241f6a02042773c8287748 +_md5_=09627e6bb74ee9997324bde01a56bcbd diff --git a/metadata/md5-cache/sci-biology/piler-1.0-r1 b/metadata/md5-cache/sci-biology/piler-1.0-r1 new file mode 100644 index 000000000000..235cd872c1bb --- /dev/null +++ b/metadata/md5-cache/sci-biology/piler-1.0-r1 @@ -0,0 +1,11 @@ +DEFINED_PHASES=configure install +DESCRIPTION=Analysis of repetitive DNA found in genome sequences +EAPI=6 +HOMEPAGE=http://www.drive5.com/piler/ +KEYWORDS=amd64 x86 +LICENSE=public-domain +RDEPEND=|| ( sci-biology/muscle sci-libs/libmuscle ) sci-biology/pals +SLOT=0 +SRC_URI=http://www.drive5.com/piler/piler_source.tar.gz -> piler-1.0.tar.gz +_eclasses_=multilib 1d91b03d42ab6308b5f4f6b598ed110e toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c +_md5_=7b5a6d618aac08240cf165a04509c319 diff --git a/metadata/md5-cache/sci-biology/pilercr-1.0-r1 b/metadata/md5-cache/sci-biology/pilercr-1.0-r1 new file mode 100644 index 000000000000..417fb3c46102 --- /dev/null +++ b/metadata/md5-cache/sci-biology/pilercr-1.0-r1 @@ -0,0 +1,10 @@ +DEFINED_PHASES=configure install +DESCRIPTION=Analysis of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) +EAPI=6 +HOMEPAGE=http://www.drive5.com/pilercr/ +KEYWORDS=amd64 x86 +LICENSE=public-domain +SLOT=0 +SRC_URI=http://www.drive5.com/pilercr/pilercr1.06.tar.gz -> pilercr-1.0.tar.gz +_eclasses_=multilib 1d91b03d42ab6308b5f4f6b598ed110e toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c +_md5_=d9f7901d3776c424cfb93782cc6ddafa diff --git a/metadata/md5-cache/sci-biology/plink-1.90_pre140514 b/metadata/md5-cache/sci-biology/plink-1.90_pre140514 new file mode 100644 index 000000000000..9364ed8f6846 --- /dev/null +++ b/metadata/md5-cache/sci-biology/plink-1.90_pre140514 @@ -0,0 +1,12 @@ +DEFINED_PHASES=compile install prepare +DEPEND=app-arch/unzip virtual/pkgconfig +DESCRIPTION=Whole genome association analysis toolset +EAPI=5 +HOMEPAGE=http://pngu.mgh.harvard.edu/~purcell/plink/ +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-2 +RDEPEND=sys-libs/zlib virtual/cblas virtual/lapack +SLOT=0 +SRC_URI=http://pngu.mgh.harvard.edu/~purcell/static/bin/plink140514/plink_src.zip -> plink-1.90_pre140514.zip +_eclasses_=desktop b1d22ac8bdd4679ab79c71aca235009d epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 1d91b03d42ab6308b5f4f6b598ed110e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=570249dc23feeff7b47b3e81df358196 diff --git a/metadata/md5-cache/sci-biology/poa-2-r1 b/metadata/md5-cache/sci-biology/poa-2-r1 new file mode 100644 index 000000000000..be51896c43ae --- /dev/null +++ b/metadata/md5-cache/sci-biology/poa-2-r1 @@ -0,0 +1,11 @@ +DEFINED_PHASES=compile install postinst prepare +DESCRIPTION=Fast multiple sequence alignments using partial-order graphs +EAPI=5 +HOMEPAGE=http://bioinfo.mbi.ucla.edu/poa/ +IUSE=static-libs +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-2 +SLOT=0 +SRC_URI=mirror://sourceforge/poamsa/poaV2.tar.gz +_eclasses_=desktop b1d22ac8bdd4679ab79c71aca235009d epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 1d91b03d42ab6308b5f4f6b598ed110e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=8c6d961d6aa6f18d30b6fb7dd995115f diff --git a/metadata/md5-cache/sci-biology/prank-140603 b/metadata/md5-cache/sci-biology/prank-140603 new file mode 100644 index 000000000000..81d6c2f91b58 --- /dev/null +++ b/metadata/md5-cache/sci-biology/prank-140603 @@ -0,0 +1,10 @@ +DEFINED_PHASES=compile install prepare +DESCRIPTION=Probabilistic Alignment Kit +EAPI=6 +HOMEPAGE=http://wasabiapp.org/software/prank/ +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-3 +SLOT=0 +SRC_URI=http://wasabiapp.org/download/prank/prank.source.140603.tgz +_eclasses_=multilib 1d91b03d42ab6308b5f4f6b598ed110e toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c +_md5_=17023476000980284365a9c0ed04a6f0 diff --git a/metadata/md5-cache/sci-biology/primer3-2.3.7 b/metadata/md5-cache/sci-biology/primer3-2.3.7 new file mode 100644 index 000000000000..318873d83263 --- /dev/null +++ b/metadata/md5-cache/sci-biology/primer3-2.3.7 @@ -0,0 +1,11 @@ +DEFINED_PHASES=compile configure install prepare test +DEPEND=dev-lang/perl +DESCRIPTION=Primer Design for PCR reactions +EAPI=6 +HOMEPAGE=http://primer3.sourceforge.net/ +KEYWORDS=~amd64 ~ppc ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris +LICENSE=GPL-2 +SLOT=0 +SRC_URI=mirror://sourceforge/project/primer3/primer3/2.3.7/primer3-2.3.7.tar.gz +_eclasses_=multilib 1d91b03d42ab6308b5f4f6b598ed110e toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c +_md5_=e79ee4774138e651c83467c2b2cb2926 diff --git a/metadata/md5-cache/sci-biology/prints-39.0-r1 b/metadata/md5-cache/sci-biology/prints-39.0-r1 new file mode 100644 index 000000000000..31cee51db19f --- /dev/null +++ b/metadata/md5-cache/sci-biology/prints-39.0-r1 @@ -0,0 +1,12 @@ +DEFINED_PHASES=compile install +DEPEND=emboss? ( sci-biology/emboss ) +DESCRIPTION=A protein motif fingerprint database +EAPI=6 +HOMEPAGE=http://www.bioinf.man.ac.uk/dbbrowser/PRINTS/ +IUSE=emboss minimal +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux +LICENSE=public-domain +RDEPEND=emboss? ( sci-biology/emboss ) +SLOT=0 +SRC_URI=mirror://gentoo/prints-39.0.tar.bz2 +_md5_=03843bbc5bed197d8df7a7bbc970230a diff --git a/metadata/md5-cache/sci-biology/probcons-1.12-r1 b/metadata/md5-cache/sci-biology/probcons-1.12-r1 new file mode 100644 index 000000000000..431c39af8362 --- /dev/null +++ b/metadata/md5-cache/sci-biology/probcons-1.12-r1 @@ -0,0 +1,11 @@ +DEFINED_PHASES=compile install postinst prepare +DESCRIPTION=Probabilistic Consistency-based Multiple Alignment of Amino Acid Sequences +EAPI=5 +HOMEPAGE=http://probcons.stanford.edu/ +KEYWORDS=amd64 x86 ~amd64-linux ~x86-linux +LICENSE=public-domain +RDEPEND=!sci-geosciences/gmt sci-visualization/gnuplot +SLOT=0 +SRC_URI=http://probcons.stanford.edu/probcons_v1_12.tar.gz +_eclasses_=desktop b1d22ac8bdd4679ab79c71aca235009d epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 1d91b03d42ab6308b5f4f6b598ed110e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=19a24bd3c543d599d5b3392e66b7022e diff --git a/metadata/md5-cache/sci-biology/prodigal-2.6.3 b/metadata/md5-cache/sci-biology/prodigal-2.6.3 new file mode 100644 index 000000000000..8ab3d00fe77a --- /dev/null +++ b/metadata/md5-cache/sci-biology/prodigal-2.6.3 @@ -0,0 +1,10 @@ +DEFINED_PHASES=configure +DESCRIPTION=Prokaryotic Dynamic Programming Genefinding Algorithm +EAPI=6 +HOMEPAGE=http://prodigal.ornl.gov/ +KEYWORDS=~amd64 +LICENSE=GPL-3 +SLOT=0 +SRC_URI=https://github.com/hyattpd/Prodigal/archive/v2.6.3.tar.gz -> prodigal-2.6.3.tar.gz +_eclasses_=multilib 1d91b03d42ab6308b5f4f6b598ed110e toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c +_md5_=9cea3bcc55e864076d7e4b542f657f96 diff --git a/metadata/md5-cache/sci-biology/profphd-1.0.39 b/metadata/md5-cache/sci-biology/profphd-1.0.39 new file mode 100644 index 000000000000..8cf832baf747 --- /dev/null +++ b/metadata/md5-cache/sci-biology/profphd-1.0.39 @@ -0,0 +1,12 @@ +DEFINED_PHASES=compile install prepare +DEPEND=dev-lang/perl +DESCRIPTION=Secondary structure and solvent accessibility predictor +EAPI=5 +HOMEPAGE=https://rostlab.org/owiki/index.php/PROFphd_-_Secondary_Structure,_Solvent_Accessibility_and_Transmembrane_Helices_Prediction +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux +LICENSE=GPL-2 +RDEPEND=dev-lang/perl dev-perl/librg-utils-perl sci-libs/profnet sci-libs/profphd-utils +SLOT=0 +SRC_URI=ftp://rostlab.org/profphd/profphd-1.0.39.tar.xz +_eclasses_=desktop b1d22ac8bdd4679ab79c71aca235009d epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 1d91b03d42ab6308b5f4f6b598ed110e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=8e866cc812e134cdc7a7837e5b60aa21 diff --git a/metadata/md5-cache/sci-biology/profphd-1.0.40 b/metadata/md5-cache/sci-biology/profphd-1.0.40 new file mode 100644 index 000000000000..512e818910f5 --- /dev/null +++ b/metadata/md5-cache/sci-biology/profphd-1.0.40 @@ -0,0 +1,12 @@ +DEFINED_PHASES=compile install prepare +DEPEND=dev-lang/perl +DESCRIPTION=Secondary structure and solvent accessibility predictor +EAPI=5 +HOMEPAGE=https://rostlab.org/owiki/index.php/PROFphd_-_Secondary_Structure,_Solvent_Accessibility_and_Transmembrane_Helices_Prediction +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux +LICENSE=GPL-2 +RDEPEND=dev-lang/perl dev-perl/librg-utils-perl sci-libs/profnet sci-libs/profphd-utils +SLOT=0 +SRC_URI=ftp://rostlab.org/profphd/profphd-1.0.40.tar.xz +_eclasses_=desktop b1d22ac8bdd4679ab79c71aca235009d epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 1d91b03d42ab6308b5f4f6b598ed110e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=b641a6cfd444fa4b83d5963246948636 diff --git a/metadata/md5-cache/sci-biology/prosite-2017.02 b/metadata/md5-cache/sci-biology/prosite-2017.02 new file mode 100644 index 000000000000..ccabbc4a37bb --- /dev/null +++ b/metadata/md5-cache/sci-biology/prosite-2017.02 @@ -0,0 +1,12 @@ +DEFINED_PHASES=compile install +DEPEND=emboss? ( sci-biology/emboss ) +DESCRIPTION=A protein families and domains database +EAPI=6 +HOMEPAGE=https://prosite.expasy.org/ +IUSE=emboss minimal +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux +LICENSE=swiss-prot +RDEPEND=emboss? ( sci-biology/emboss ) +SLOT=0 +SRC_URI=ftp://ftp.expasy.org/databases/prosite/old_releases/prosite2017_02.tar.bz2 +_md5_=e37bd9f81e9458715d22a6138fb2029a diff --git a/metadata/md5-cache/sci-biology/psipred-3.4 b/metadata/md5-cache/sci-biology/psipred-3.4 new file mode 100644 index 000000000000..c1c044c6a714 --- /dev/null +++ b/metadata/md5-cache/sci-biology/psipred-3.4 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile install postinst prepare +DESCRIPTION=Protein Secondary Structure Prediction +EAPI=5 +HOMEPAGE=http://bioinf.cs.ucl.ac.uk/psipred/ +IUSE=test +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux +LICENSE=psipred +RDEPEND=app-shells/tcsh sci-biology/ncbi-tools sci-biology/update-blastdb +RESTRICT=!test? ( test ) +SLOT=0 +SRC_URI=http://bioinf.cs.ucl.ac.uk/downloads/psipred/psipred3.4.tar.gz test? ( http://bioinfadmin.cs.ucl.ac.uk/downloads/psipred/old/data/tdbdata.tar.gz ) +_eclasses_=desktop b1d22ac8bdd4679ab79c71aca235009d epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 1d91b03d42ab6308b5f4f6b598ed110e prefix c2993e4c430c1ee24f278983d6189501 preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf versionator 2352c3fc97241f6a02042773c8287748 +_md5_=44623bcd0b50824824056739420b4873 diff --git a/metadata/md5-cache/sci-biology/psipred-3.5 b/metadata/md5-cache/sci-biology/psipred-3.5 new file mode 100644 index 000000000000..b4ec14863bfb --- /dev/null +++ b/metadata/md5-cache/sci-biology/psipred-3.5 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile install postinst prepare +DESCRIPTION=Protein Secondary Structure Prediction +EAPI=5 +HOMEPAGE=http://bioinf.cs.ucl.ac.uk/psipred/ +IUSE=test +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux +LICENSE=psipred +RDEPEND=app-shells/tcsh sci-biology/ncbi-tools sci-biology/update-blastdb +RESTRICT=!test? ( test ) +SLOT=0 +SRC_URI=http://bioinf.cs.ucl.ac.uk/downloads/psipred/psipred3.5.tar.gz test? ( http://bioinfadmin.cs.ucl.ac.uk/downloads/psipred/old/data/tdbdata.tar.gz ) +_eclasses_=desktop b1d22ac8bdd4679ab79c71aca235009d epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 1d91b03d42ab6308b5f4f6b598ed110e prefix c2993e4c430c1ee24f278983d6189501 preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf versionator 2352c3fc97241f6a02042773c8287748 +_md5_=44623bcd0b50824824056739420b4873 diff --git a/metadata/md5-cache/sci-biology/pysam-0.12.0.1 b/metadata/md5-cache/sci-biology/pysam-0.12.0.1 new file mode 100644 index 000000000000..7ee1800a9e63 --- /dev/null +++ b/metadata/md5-cache/sci-biology/pysam-0.12.0.1 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile configure install prepare test +DEPEND==sci-libs/htslib-1.5*:= dev-python/cython[python_targets_python2_7(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_6(-)] dev-python/setuptools[python_targets_python2_7(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_6(-)] python_targets_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 ) python_targets_python3_6? ( dev-lang/python:3.6 ) >=dev-lang/python-exec-2:=[python_targets_python2_7(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_6(-)] dev-python/setuptools[python_targets_python2_7(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_6(-)] +DESCRIPTION=Python interface for the SAM/BAM sequence alignment and mapping format +EAPI=6 +HOMEPAGE=https://github.com/pysam-developers/pysam https://pypi.org/project/pysam/ +IUSE=python_targets_python2_7 python_targets_python3_6 +KEYWORDS=~amd64 ~x86 +LICENSE=MIT +RDEPEND==sci-libs/htslib-1.5*:= python_targets_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 ) python_targets_python3_6? ( dev-lang/python:3.6 ) >=dev-lang/python-exec-2:=[python_targets_python2_7(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_6(-)] +REQUIRED_USE=|| ( python_targets_python2_7 python_targets_python3_6 ) +SLOT=0 +SRC_URI=mirror://pypi/p/pysam/pysam-0.12.0.1.tar.gz +_eclasses_=desktop b1d22ac8bdd4679ab79c71aca235009d distutils-r1 c576838cd67e384002a18edd54be710e epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 ltprune 2729691420b6deeda2a90b1f1183fb55 multibuild 40fe59465edacd730c644ec2bc197809 multilib 1d91b03d42ab6308b5f4f6b598ed110e multiprocessing cac3169468f893670dac3e7cb940e045 preserve-libs ef207dc62baddfddfd39a164d9797648 python-r1 4eed5e0c72d4544a2291ae46515f5d79 python-utils-r1 611c493a4cfef5254350fabc04b606f5 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf xdg-utils ff2ff954e6b17929574eee4efc5152ba +_md5_=3982e194da0412a02dc76e2431b051de diff --git a/metadata/md5-cache/sci-biology/qrna-2.0.3c-r3 b/metadata/md5-cache/sci-biology/qrna-2.0.3c-r3 new file mode 100644 index 000000000000..161478242c95 --- /dev/null +++ b/metadata/md5-cache/sci-biology/qrna-2.0.3c-r3 @@ -0,0 +1,12 @@ +DEFINED_PHASES=compile install prepare +DEPEND=dev-lang/perl sci-biology/hmmer:2 +DESCRIPTION=Prototype ncRNA genefinder +EAPI=6 +HOMEPAGE=http://selab.janelia.org/software.html +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-2 +RDEPEND=dev-lang/perl sci-biology/hmmer:2 +SLOT=0 +SRC_URI=mirror://gentoo/qrna-2.0.3c.tar.bz2 +_eclasses_=multilib 1d91b03d42ab6308b5f4f6b598ed110e toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c +_md5_=0fc8dac0f54d22c60da996470b3b33ee diff --git a/metadata/md5-cache/sci-biology/raxml-7.2.6 b/metadata/md5-cache/sci-biology/raxml-7.2.6 new file mode 100644 index 000000000000..8afd58db68c2 --- /dev/null +++ b/metadata/md5-cache/sci-biology/raxml-7.2.6 @@ -0,0 +1,12 @@ +DEFINED_PHASES=compile install prepare +DESCRIPTION=Sequential, Parallel & Distributed Inference of Large Phylogenetic Trees +EAPI=5 +HOMEPAGE=http://wwwkramer.in.tum.de/exelixis/software.html +IUSE=cpu_flags_x86_sse3 +threads +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-2 +REQUIRED_USE=cpu_flags_x86_sse3 +SLOT=0 +SRC_URI=http://wwwkramer.in.tum.de/exelixis/software/RAxML-7.2.6.tar.bz2 +_eclasses_=desktop b1d22ac8bdd4679ab79c71aca235009d epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 flag-o-matic dc34234e8c43343da45853da22dcf14b ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 1d91b03d42ab6308b5f4f6b598ed110e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=f2b8e0b4e5701d9b20bcbf9151c9b868 diff --git a/metadata/md5-cache/sci-biology/rebase-1701 b/metadata/md5-cache/sci-biology/rebase-1701 new file mode 100644 index 000000000000..d86bf89d9ab9 --- /dev/null +++ b/metadata/md5-cache/sci-biology/rebase-1701 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile install +DEPEND=emboss? ( >=sci-biology/emboss-5.0.0 ) +DESCRIPTION=A restriction enzyme database +EAPI=6 +HOMEPAGE=http://rebase.neb.com +IUSE=emboss minimal +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux +LICENSE=public-domain +RDEPEND=emboss? ( >=sci-biology/emboss-5.0.0 ) +RESTRICT=binchecks strip +SLOT=0 +SRC_URI=https://dev.gentoo.org/~jlec/distfiles/rebase-1701.tar.xz +_md5_=68457638d36f4995a29fb959283e85a4 diff --git a/metadata/md5-cache/sci-biology/rebase-1702 b/metadata/md5-cache/sci-biology/rebase-1702 new file mode 100644 index 000000000000..b16c62f4e2fa --- /dev/null +++ b/metadata/md5-cache/sci-biology/rebase-1702 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile install +DEPEND=emboss? ( >=sci-biology/emboss-5.0.0 ) +DESCRIPTION=A restriction enzyme database +EAPI=6 +HOMEPAGE=http://rebase.neb.com +IUSE=emboss minimal +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris ~x86-solaris +LICENSE=public-domain +RDEPEND=emboss? ( >=sci-biology/emboss-5.0.0 ) +RESTRICT=binchecks strip +SLOT=0 +SRC_URI=https://dev.gentoo.org/~jlec/distfiles/rebase-1702.tar.xz +_md5_=b934757ccdbd2999376f90a29fabbeb5 diff --git a/metadata/md5-cache/sci-biology/rebase-1703 b/metadata/md5-cache/sci-biology/rebase-1703 new file mode 100644 index 000000000000..5172f9e323ca --- /dev/null +++ b/metadata/md5-cache/sci-biology/rebase-1703 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile install +DEPEND=emboss? ( >=sci-biology/emboss-5.0.0 ) +DESCRIPTION=A restriction enzyme database +EAPI=6 +HOMEPAGE=http://rebase.neb.com +IUSE=emboss minimal +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris ~x86-solaris +LICENSE=public-domain +RDEPEND=emboss? ( >=sci-biology/emboss-5.0.0 ) +RESTRICT=binchecks strip +SLOT=0 +SRC_URI=https://dev.gentoo.org/~jlec/distfiles/rebase-1703.tar.xz +_md5_=b934757ccdbd2999376f90a29fabbeb5 diff --git a/metadata/md5-cache/sci-biology/rebase-1704 b/metadata/md5-cache/sci-biology/rebase-1704 new file mode 100644 index 000000000000..4165b701add8 --- /dev/null +++ b/metadata/md5-cache/sci-biology/rebase-1704 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile install +DEPEND=emboss? ( >=sci-biology/emboss-5.0.0 ) +DESCRIPTION=A restriction enzyme database +EAPI=6 +HOMEPAGE=http://rebase.neb.com +IUSE=emboss minimal +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris ~x86-solaris +LICENSE=public-domain +RDEPEND=emboss? ( >=sci-biology/emboss-5.0.0 ) +RESTRICT=binchecks strip +SLOT=0 +SRC_URI=https://dev.gentoo.org/~jlec/distfiles/rebase-1704.tar.xz +_md5_=b934757ccdbd2999376f90a29fabbeb5 diff --git a/metadata/md5-cache/sci-biology/rebase-1803 b/metadata/md5-cache/sci-biology/rebase-1803 new file mode 100644 index 000000000000..e04f8ae6b53d --- /dev/null +++ b/metadata/md5-cache/sci-biology/rebase-1803 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile install +DEPEND=emboss? ( >=sci-biology/emboss-5.0.0 ) +DESCRIPTION=A restriction enzyme database +EAPI=6 +HOMEPAGE=http://rebase.neb.com +IUSE=emboss minimal +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris ~x86-solaris +LICENSE=public-domain +RDEPEND=emboss? ( >=sci-biology/emboss-5.0.0 ) +RESTRICT=binchecks strip +SLOT=0 +SRC_URI=https://dev.gentoo.org/~jlec/distfiles/rebase-1803.tar.xz +_md5_=03338bf80d0fb82894ab8e39e00b1898 diff --git a/metadata/md5-cache/sci-biology/rebase-1806 b/metadata/md5-cache/sci-biology/rebase-1806 new file mode 100644 index 000000000000..8eeafd55e477 --- /dev/null +++ b/metadata/md5-cache/sci-biology/rebase-1806 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile install +DEPEND=emboss? ( >=sci-biology/emboss-5.0.0 ) +DESCRIPTION=A restriction enzyme database +EAPI=6 +HOMEPAGE=http://rebase.neb.com +IUSE=emboss minimal +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris ~x86-solaris +LICENSE=public-domain +RDEPEND=emboss? ( >=sci-biology/emboss-5.0.0 ) +RESTRICT=binchecks strip +SLOT=0 +SRC_URI=https://dev.gentoo.org/~jlec/distfiles/rebase-1806.tar.xz +_md5_=03338bf80d0fb82894ab8e39e00b1898 diff --git a/metadata/md5-cache/sci-biology/rebase-1810 b/metadata/md5-cache/sci-biology/rebase-1810 new file mode 100644 index 000000000000..377675de0e57 --- /dev/null +++ b/metadata/md5-cache/sci-biology/rebase-1810 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile install +DEPEND=emboss? ( >=sci-biology/emboss-5.0.0 ) +DESCRIPTION=A restriction enzyme database +EAPI=6 +HOMEPAGE=http://rebase.neb.com +IUSE=emboss minimal +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris ~x86-solaris +LICENSE=public-domain +RDEPEND=emboss? ( >=sci-biology/emboss-5.0.0 ) +RESTRICT=binchecks strip +SLOT=0 +SRC_URI=https://dev.gentoo.org/~jlec/distfiles/rebase-1810.tar.xz +_md5_=03338bf80d0fb82894ab8e39e00b1898 diff --git a/metadata/md5-cache/sci-biology/rebase-1901 b/metadata/md5-cache/sci-biology/rebase-1901 new file mode 100644 index 000000000000..b5a635750eee --- /dev/null +++ b/metadata/md5-cache/sci-biology/rebase-1901 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile install +DEPEND=emboss? ( >=sci-biology/emboss-5.0.0 ) +DESCRIPTION=A restriction enzyme database +EAPI=6 +HOMEPAGE=http://rebase.neb.com +IUSE=emboss minimal +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris ~x86-solaris +LICENSE=public-domain +RDEPEND=emboss? ( >=sci-biology/emboss-5.0.0 ) +RESTRICT=binchecks strip +SLOT=0 +SRC_URI=https://dev.gentoo.org/~jlec/distfiles/rebase-1901.tar.xz +_md5_=af6eb0bdb9d763276057136d501fc836 diff --git a/metadata/md5-cache/sci-biology/recon-1.08 b/metadata/md5-cache/sci-biology/recon-1.08 new file mode 100644 index 000000000000..27c84335bf86 --- /dev/null +++ b/metadata/md5-cache/sci-biology/recon-1.08 @@ -0,0 +1,12 @@ +DEFINED_PHASES=compile install prepare +DESCRIPTION=Automated de novo identification of repeat families from genomic sequences +EAPI=6 +HOMEPAGE=http://www.repeatmasker.org/RepeatModeler.html +IUSE=examples +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-2 +RDEPEND=dev-lang/perl +SLOT=0 +SRC_URI=http://www.repeatmasker.org/RECON-1.08.tar.gz +_eclasses_=multilib 1d91b03d42ab6308b5f4f6b598ed110e toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c +_md5_=2ddd537d912c7c88b6f0b0d203a51613 diff --git a/metadata/md5-cache/sci-biology/repeatmasker-4.0.1 b/metadata/md5-cache/sci-biology/repeatmasker-4.0.1 new file mode 100644 index 000000000000..901277aaf4b1 --- /dev/null +++ b/metadata/md5-cache/sci-biology/repeatmasker-4.0.1 @@ -0,0 +1,10 @@ +DEFINED_PHASES=configure install +DESCRIPTION=Screen DNA sequences for interspersed repeats and low complexity DNA +EAPI=5 +HOMEPAGE=http://repeatmasker.org/ +KEYWORDS=~amd64 ~x86 +LICENSE=OSL-2.1 +RDEPEND=sci-biology/rmblast sci-biology/trf sci-biology/repeatmasker-libraries +SLOT=0 +SRC_URI=http://www.repeatmasker.org/RepeatMasker-open-4-0-1.tar.gz +_md5_=fb121561694712a9551278581c495f9c diff --git a/metadata/md5-cache/sci-biology/repeatmasker-libraries-20120418 b/metadata/md5-cache/sci-biology/repeatmasker-libraries-20120418 new file mode 100644 index 000000000000..a1dfb6bb2bee --- /dev/null +++ b/metadata/md5-cache/sci-biology/repeatmasker-libraries-20120418 @@ -0,0 +1,10 @@ +DEFINED_PHASES=install nofetch +DESCRIPTION=A special version of RepBase used by RepeatMasker +EAPI=5 +HOMEPAGE=http://repeatmasker.org/ +KEYWORDS=~amd64 ~x86 +LICENSE=all-rights-reserved +RESTRICT=fetch +SLOT=0 +SRC_URI=repeatmaskerlibraries-20120418.tar.gz +_md5_=58d2bc25a79cc7136e64f302004caa16 diff --git a/metadata/md5-cache/sci-biology/rmblast-1.2-r1 b/metadata/md5-cache/sci-biology/rmblast-1.2-r1 new file mode 100644 index 000000000000..7f6fa81c34d3 --- /dev/null +++ b/metadata/md5-cache/sci-biology/rmblast-1.2-r1 @@ -0,0 +1,12 @@ +DEFINED_PHASES=configure prepare +DEPEND=dev-libs/boost app-arch/cpio +DESCRIPTION=RepeatMasker compatible version of NCBI BLAST+ +EAPI=5 +HOMEPAGE=http://www.repeatmasker.org/RMBlast.html +KEYWORDS=~amd64 ~x86 +LICENSE=OSL-2.1 +RDEPEND=dev-libs/boost +SLOT=0 +SRC_URI=http://www.repeatmasker.org/rmblast-1.2-ncbi-blast-2.2.23+-src.tar.gz https://dev.gentoo.org/~mgorny/dist/rmblast-1.2-gcc47.patch.bz2 +_eclasses_=desktop b1d22ac8bdd4679ab79c71aca235009d epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 flag-o-matic dc34234e8c43343da45853da22dcf14b ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 1d91b03d42ab6308b5f4f6b598ed110e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=1283e94bf3a231a794a498d2769aaa7d diff --git a/metadata/md5-cache/sci-biology/rnaview-20040713-r4 b/metadata/md5-cache/sci-biology/rnaview-20040713-r4 new file mode 100644 index 000000000000..f8d9227b36e8 --- /dev/null +++ b/metadata/md5-cache/sci-biology/rnaview-20040713-r4 @@ -0,0 +1,10 @@ +DEFINED_PHASES=install prepare +DESCRIPTION=Generates 2D displays of RNA/DNA secondary structures with tertiary interactions +EAPI=6 +HOMEPAGE=http://ndbserver.rutgers.edu/services/download/index.html +KEYWORDS=~amd64 ~x86 +LICENSE=public-domain +SLOT=0 +SRC_URI=mirror://gentoo/rnaview-20040713.tar.bz2 +_eclasses_=multilib 1d91b03d42ab6308b5f4f6b598ed110e toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c +_md5_=788c156d45287bef4f6aa876055bde4c diff --git a/metadata/md5-cache/sci-biology/samtools-0.1.20-r3 b/metadata/md5-cache/sci-biology/samtools-0.1.20-r3 new file mode 100644 index 000000000000..6e19d460f95a --- /dev/null +++ b/metadata/md5-cache/sci-biology/samtools-0.1.20-r3 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile install postinst prepare setup +DEPEND=python_single_target_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 >=dev-lang/python-exec-2:=[python_targets_python2_7] ) sys-libs/ncurses:0= dev-lang/perl virtual/pkgconfig +DESCRIPTION=Utilities for analysing and manipulating the SAM/BAM alignment formats +EAPI=6 +HOMEPAGE=http://samtools.sourceforge.net/ +IUSE=examples +python_targets_python2_7 +python_single_target_python2_7 +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos +LICENSE=MIT +RDEPEND=python_single_target_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 >=dev-lang/python-exec-2:=[python_targets_python2_7] ) sys-libs/ncurses:0= dev-lang/perl +REQUIRED_USE=^^ ( python_single_target_python2_7 ) python_single_target_python2_7? ( python_targets_python2_7 ) +SLOT=0.1-legacy +SRC_URI=https://github.com/samtools/samtools/archive/0.1.20.tar.gz -> samtools-0.1.20.tar.gz +_eclasses_=multilib 1d91b03d42ab6308b5f4f6b598ed110e python-single-r1 36ac48e647d2627de28c87aaffb94753 python-utils-r1 611c493a4cfef5254350fabc04b606f5 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c +_md5_=fa48f0b2be780a9264eb9d727ec53335 diff --git a/metadata/md5-cache/sci-biology/samtools-1.5 b/metadata/md5-cache/sci-biology/samtools-1.5 new file mode 100644 index 000000000000..fdf66c5cec3e --- /dev/null +++ b/metadata/md5-cache/sci-biology/samtools-1.5 @@ -0,0 +1,14 @@ +DEFINED_PHASES=install prepare test +DEPEND=dev-lang/perl =sci-libs/htslib-1.5* sys-libs/ncurses:0= sys-libs/zlib python_targets_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 ) >=dev-lang/python-exec-2:=[python_targets_python2_7(-)?,-python_single_target_python2_7(-)] virtual/pkgconfig >=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 +DESCRIPTION=Utilities for analysing and manipulating the SAM/BAM alignment formats +EAPI=6 +HOMEPAGE=http://www.htslib.org/ +IUSE=examples python_targets_python2_7 +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos +LICENSE=MIT +RDEPEND=dev-lang/perl =sci-libs/htslib-1.5* sys-libs/ncurses:0= sys-libs/zlib python_targets_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 ) >=dev-lang/python-exec-2:=[python_targets_python2_7(-)?,-python_single_target_python2_7(-)] +REQUIRED_USE=|| ( python_targets_python2_7 ) +SLOT=0 +SRC_URI=mirror://sourceforge/samtools/samtools-1.5.tar.bz2 +_eclasses_=autotools ea7865c8fba1ea8d3639f355fffe1a3c libtool f143db5a74ccd9ca28c1234deffede96 multibuild 40fe59465edacd730c644ec2bc197809 multilib 1d91b03d42ab6308b5f4f6b598ed110e python-r1 4eed5e0c72d4544a2291ae46515f5d79 python-utils-r1 611c493a4cfef5254350fabc04b606f5 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c +_md5_=8d92b4a814f62eab87bac2be22c2470c diff --git a/metadata/md5-cache/sci-biology/samtools-1.9 b/metadata/md5-cache/sci-biology/samtools-1.9 new file mode 100644 index 000000000000..763cf4ac915a --- /dev/null +++ b/metadata/md5-cache/sci-biology/samtools-1.9 @@ -0,0 +1,15 @@ +BDEPEND=>=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 +DEFINED_PHASES=install prepare setup test +DEPEND=dev-lang/perl =sci-libs/htslib-1.9* sys-libs/ncurses:0= sys-libs/zlib:= python_single_target_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 >=dev-lang/python-exec-2:=[python_targets_python2_7] ) virtual/pkgconfig +DESCRIPTION=Utilities for analysing and manipulating the SAM/BAM alignment formats +EAPI=7 +HOMEPAGE=http://www.htslib.org/ +IUSE=examples +python_targets_python2_7 +python_single_target_python2_7 +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos +LICENSE=MIT +RDEPEND=dev-lang/perl =sci-libs/htslib-1.9* sys-libs/ncurses:0= sys-libs/zlib:= python_single_target_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 >=dev-lang/python-exec-2:=[python_targets_python2_7] ) +REQUIRED_USE=^^ ( python_single_target_python2_7 ) python_single_target_python2_7? ( python_targets_python2_7 ) +SLOT=0 +SRC_URI=mirror://sourceforge/samtools/samtools-1.9.tar.bz2 +_eclasses_=autotools ea7865c8fba1ea8d3639f355fffe1a3c libtool f143db5a74ccd9ca28c1234deffede96 multilib 1d91b03d42ab6308b5f4f6b598ed110e python-single-r1 36ac48e647d2627de28c87aaffb94753 python-utils-r1 611c493a4cfef5254350fabc04b606f5 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c +_md5_=7e8913a97cbbcf5ee0158a89a42fa92c diff --git a/metadata/md5-cache/sci-biology/seaview-4.3.5 b/metadata/md5-cache/sci-biology/seaview-4.3.5 new file mode 100644 index 000000000000..ac0b50b109d4 --- /dev/null +++ b/metadata/md5-cache/sci-biology/seaview-4.3.5 @@ -0,0 +1,13 @@ +DEFINED_PHASES=install prepare +DEPEND=sys-libs/zlib x11-libs/fltk:1 x11-libs/libX11 xft? ( x11-libs/libXft x11-libs/fltk:1[xft] ) virtual/pkgconfig +DESCRIPTION=A graphical multiple sequence alignment editor +EAPI=5 +HOMEPAGE=http://pbil.univ-lyon1.fr/software/seaview.html +IUSE=+xft +KEYWORDS=amd64 x86 +LICENSE=public-domain +RDEPEND=sys-libs/zlib x11-libs/fltk:1 x11-libs/libX11 xft? ( x11-libs/libXft x11-libs/fltk:1[xft] ) sci-biology/clustalw || ( sci-libs/libmuscle sci-biology/muscle ) sci-biology/phyml +SLOT=0 +SRC_URI=ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/seaview_4.3.5.tar.gz +_eclasses_=desktop b1d22ac8bdd4679ab79c71aca235009d epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 1d91b03d42ab6308b5f4f6b598ed110e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=38cc02682d853c813df2b6e81cbb51c5 diff --git a/metadata/md5-cache/sci-biology/seaview-4.5.4 b/metadata/md5-cache/sci-biology/seaview-4.5.4 new file mode 100644 index 000000000000..193b47dc7c2a --- /dev/null +++ b/metadata/md5-cache/sci-biology/seaview-4.5.4 @@ -0,0 +1,13 @@ +DEFINED_PHASES=install prepare +DEPEND=sys-libs/zlib x11-libs/fltk:1 x11-libs/libX11 xft? ( x11-libs/libXft x11-libs/fltk:1[xft] ) virtual/pkgconfig +DESCRIPTION=A graphical multiple sequence alignment editor +EAPI=5 +HOMEPAGE=http://pbil.univ-lyon1.fr/software/seaview.html +IUSE=+xft +KEYWORDS=amd64 x86 +LICENSE=public-domain +RDEPEND=sys-libs/zlib x11-libs/fltk:1 x11-libs/libX11 xft? ( x11-libs/libXft x11-libs/fltk:1[xft] ) sci-biology/clustalw || ( sci-libs/libmuscle sci-biology/muscle ) sci-biology/phyml +SLOT=0 +SRC_URI=ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/seaview_4.5.4.tar.gz +_eclasses_=desktop b1d22ac8bdd4679ab79c71aca235009d epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 1d91b03d42ab6308b5f4f6b598ed110e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=38cc02682d853c813df2b6e81cbb51c5 diff --git a/metadata/md5-cache/sci-biology/seaview-4.6 b/metadata/md5-cache/sci-biology/seaview-4.6 new file mode 100644 index 000000000000..3f782aafb644 --- /dev/null +++ b/metadata/md5-cache/sci-biology/seaview-4.6 @@ -0,0 +1,13 @@ +DEFINED_PHASES=install prepare +DEPEND=sys-libs/zlib x11-libs/fltk:1 x11-libs/libX11 xft? ( x11-libs/libXft x11-libs/fltk:1[xft] ) sci-biology/clustalw:2 || ( sci-libs/libmuscle sci-biology/muscle ) sci-biology/phyml virtual/pkgconfig +DESCRIPTION=A graphical multiple sequence alignment editor +EAPI=6 +HOMEPAGE=http://pbil.univ-lyon1.fr/software/seaview.html +IUSE=+xft +KEYWORDS=~amd64 ~x86 +LICENSE=public-domain +RDEPEND=sys-libs/zlib x11-libs/fltk:1 x11-libs/libX11 xft? ( x11-libs/libXft x11-libs/fltk:1[xft] ) sci-biology/clustalw:2 || ( sci-libs/libmuscle sci-biology/muscle ) sci-biology/phyml +SLOT=0 +SRC_URI=ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/seaview_4.6.tar.gz +_eclasses_=desktop b1d22ac8bdd4679ab79c71aca235009d epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 1d91b03d42ab6308b5f4f6b598ed110e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=1a6723f1ab0e67cc0d63dd54a902900f diff --git a/metadata/md5-cache/sci-biology/seqan-1.4.2-r1 b/metadata/md5-cache/sci-biology/seqan-1.4.2-r1 new file mode 100644 index 000000000000..faf0ca0a7dcc --- /dev/null +++ b/metadata/md5-cache/sci-biology/seqan-1.4.2-r1 @@ -0,0 +1,15 @@ +DEFINED_PHASES=compile configure install postinst prepare setup test +DEPEND=app-arch/bzip2 sys-libs/zlib test? ( || ( ( >=dev-lang/python-2.7.5-r2:2.7 dev-python/nose[python_targets_python2_7(-),python_single_target_python2_7(+)] ) ) || ( >=dev-lang/python-2.7.5-r2:2.7 ) ) sys-devel/make >=dev-util/cmake-3.9.6 +DESCRIPTION=C++ Sequence Analysis Library +EAPI=6 +HOMEPAGE=http://www.seqan.de/ +IUSE=cpu_flags_x86_sse4_1 test +KEYWORDS=amd64 x86 ~amd64-linux ~x86-linux +LICENSE=BSD GPL-3 +RDEPEND=app-arch/bzip2 sys-libs/zlib +REQUIRED_USE=cpu_flags_x86_sse4_1 +RESTRICT=!test? ( test ) +SLOT=1.4 +SRC_URI=http://packages.seqan.de/seqan-src/seqan-src-1.4.2.tar.gz +_eclasses_=cmake-utils be72eac95bd029ad1d81d5d656c3c83b desktop b1d22ac8bdd4679ab79c71aca235009d epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 flag-o-matic dc34234e8c43343da45853da22dcf14b ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 1d91b03d42ab6308b5f4f6b598ed110e multiprocessing cac3169468f893670dac3e7cb940e045 ninja-utils 132cbb376048d079b5a012f5467c4e7f preserve-libs ef207dc62baddfddfd39a164d9797648 python-any-r1 b6db354660033efd06cd6d7f4905ccea python-utils-r1 611c493a4cfef5254350fabc04b606f5 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf versionator 2352c3fc97241f6a02042773c8287748 xdg-utils ff2ff954e6b17929574eee4efc5152ba +_md5_=1f1cf11ee07a7961e6fa23345e516b65 diff --git a/metadata/md5-cache/sci-biology/seqan-2.2.0-r1 b/metadata/md5-cache/sci-biology/seqan-2.2.0-r1 new file mode 100644 index 000000000000..b60c2fac3077 --- /dev/null +++ b/metadata/md5-cache/sci-biology/seqan-2.2.0-r1 @@ -0,0 +1,15 @@ +DEFINED_PHASES=compile configure install prepare setup test +DEPEND=app-arch/bzip2 sys-libs/zlib !!sci-biology/seqan:2.0 !!sci-biology/seqan:2.1 !!sci-biology/seqan:2.2 doc? ( || ( ( >=dev-lang/python-2.7.5-r2:2.7 dev-python/sphinx[python_targets_python2_7(-),python_single_target_python2_7(+)] ) ) || ( >=dev-lang/python-2.7.5-r2:2.7 ) ) test? ( || ( ( >=dev-lang/python-2.7.5-r2:2.7 dev-python/nose[python_targets_python2_7(-),python_single_target_python2_7(+)] ) ) || ( >=dev-lang/python-2.7.5-r2:2.7 ) ) sys-devel/make >=dev-util/cmake-3.9.6 +DESCRIPTION=C++ Sequence Analysis Library +EAPI=6 +HOMEPAGE=http://www.seqan.de/ +IUSE=cpu_flags_x86_sse4_1 doc test +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux +LICENSE=BSD GPL-3 +RDEPEND=app-arch/bzip2 sys-libs/zlib !!sci-biology/seqan:2.0 !!sci-biology/seqan:2.1 !!sci-biology/seqan:2.2 +REQUIRED_USE=cpu_flags_x86_sse4_1 +RESTRICT=!test? ( test ) +SLOT=0 +SRC_URI=http://packages.seqan.de/seqan-src/seqan-src-2.2.0.tar.gz +_eclasses_=cmake-utils be72eac95bd029ad1d81d5d656c3c83b desktop b1d22ac8bdd4679ab79c71aca235009d epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 flag-o-matic dc34234e8c43343da45853da22dcf14b ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 1d91b03d42ab6308b5f4f6b598ed110e multiprocessing cac3169468f893670dac3e7cb940e045 ninja-utils 132cbb376048d079b5a012f5467c4e7f preserve-libs ef207dc62baddfddfd39a164d9797648 python-any-r1 b6db354660033efd06cd6d7f4905ccea python-utils-r1 611c493a4cfef5254350fabc04b606f5 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf versionator 2352c3fc97241f6a02042773c8287748 xdg-utils ff2ff954e6b17929574eee4efc5152ba +_md5_=16bcf021b05ae673eb5878cdcefd8d8c diff --git a/metadata/md5-cache/sci-biology/seqan-2.4.0 b/metadata/md5-cache/sci-biology/seqan-2.4.0 new file mode 100644 index 000000000000..42f46c3ba117 --- /dev/null +++ b/metadata/md5-cache/sci-biology/seqan-2.4.0 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile configure install prepare setup test +DEPEND=app-arch/bzip2:= sys-libs/zlib:= !!sci-biology/seqan:2.0 !!sci-biology/seqan:2.1 !!sci-biology/seqan:2.2 doc? ( || ( ( >=dev-lang/python-2.7.5-r2:2.7 dev-python/sphinx[python_targets_python2_7(-),python_single_target_python2_7(+)] ) ) || ( >=dev-lang/python-2.7.5-r2:2.7 ) ) dev-util/ninja >=dev-util/cmake-3.9.6 +DESCRIPTION=C++ Sequence Analysis Library +EAPI=6 +HOMEPAGE=http://www.seqan.de/ +IUSE=cpu_flags_x86_sse4_1 doc tools +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux +LICENSE=BSD GPL-3 +RDEPEND=app-arch/bzip2:= sys-libs/zlib:= !!sci-biology/seqan:2.0 !!sci-biology/seqan:2.1 !!sci-biology/seqan:2.2 +REQUIRED_USE=cpu_flags_x86_sse4_1 +SLOT=0 +SRC_URI=https://github.com/seqan/seqan/archive/seqan-v2.4.0.tar.gz +_eclasses_=cmake-utils be72eac95bd029ad1d81d5d656c3c83b desktop b1d22ac8bdd4679ab79c71aca235009d epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 flag-o-matic dc34234e8c43343da45853da22dcf14b ltprune 2729691420b6deeda2a90b1f1183fb55 multibuild 40fe59465edacd730c644ec2bc197809 multilib 1d91b03d42ab6308b5f4f6b598ed110e multiprocessing cac3169468f893670dac3e7cb940e045 ninja-utils 132cbb376048d079b5a012f5467c4e7f preserve-libs ef207dc62baddfddfd39a164d9797648 python-any-r1 b6db354660033efd06cd6d7f4905ccea python-utils-r1 611c493a4cfef5254350fabc04b606f5 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf xdg-utils ff2ff954e6b17929574eee4efc5152ba +_md5_=ca34cde2b2fc2f8692469a016bc077f6 diff --git a/metadata/md5-cache/sci-biology/seqan-9999 b/metadata/md5-cache/sci-biology/seqan-9999 new file mode 100644 index 000000000000..6170cc9e8015 --- /dev/null +++ b/metadata/md5-cache/sci-biology/seqan-9999 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile configure install prepare setup test unpack +DEPEND=app-arch/bzip2:= sys-libs/zlib:= !!sci-biology/seqan:2.0 !!sci-biology/seqan:2.1 !!sci-biology/seqan:2.2 doc? ( || ( ( >=dev-lang/python-2.7.5-r2:2.7 dev-python/sphinx[python_targets_python2_7(-),python_single_target_python2_7(+)] ) ) || ( >=dev-lang/python-2.7.5-r2:2.7 ) ) dev-util/ninja >=dev-util/cmake-3.9.6 >=dev-vcs/git-1.8.2.1[curl] +DESCRIPTION=C++ Sequence Analysis Library +EAPI=6 +HOMEPAGE=http://www.seqan.de/ +IUSE=cpu_flags_x86_sse4_1 doc tools +LICENSE=BSD GPL-3 +PROPERTIES=live +RDEPEND=app-arch/bzip2:= sys-libs/zlib:= !!sci-biology/seqan:2.0 !!sci-biology/seqan:2.1 !!sci-biology/seqan:2.2 +REQUIRED_USE=cpu_flags_x86_sse4_1 +SLOT=0 +_eclasses_=cmake-utils be72eac95bd029ad1d81d5d656c3c83b desktop b1d22ac8bdd4679ab79c71aca235009d epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 flag-o-matic dc34234e8c43343da45853da22dcf14b git-r3 809e27702c573cbba31c08ed00bbad33 ltprune 2729691420b6deeda2a90b1f1183fb55 multibuild 40fe59465edacd730c644ec2bc197809 multilib 1d91b03d42ab6308b5f4f6b598ed110e multiprocessing cac3169468f893670dac3e7cb940e045 ninja-utils 132cbb376048d079b5a012f5467c4e7f preserve-libs ef207dc62baddfddfd39a164d9797648 python-any-r1 b6db354660033efd06cd6d7f4905ccea python-utils-r1 611c493a4cfef5254350fabc04b606f5 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf xdg-utils ff2ff954e6b17929574eee4efc5152ba +_md5_=954c2a9b05e60f6a61eb27c1cc720117 diff --git a/metadata/md5-cache/sci-biology/shrimp-2.2.3 b/metadata/md5-cache/sci-biology/shrimp-2.2.3 new file mode 100644 index 000000000000..4241a49b91d8 --- /dev/null +++ b/metadata/md5-cache/sci-biology/shrimp-2.2.3 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile install prepare pretend setup +DEPEND=!sci-mathematics/cado-nfs +DESCRIPTION=SHort Read Mapping Package +EAPI=5 +HOMEPAGE=http://compbio.cs.toronto.edu/shrimp/ +IUSE=custom-cflags +cpu_flags_x86_sse2 +python_targets_python2_7 +python_single_target_python2_7 +KEYWORDS=~amd64 ~x86 +LICENSE=shrimp +RDEPEND=!sci-mathematics/cado-nfs python_single_target_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 >=dev-lang/python-exec-2:=[python_targets_python2_7] ) +REQUIRED_USE=^^ ( python_single_target_python2_7 ) python_single_target_python2_7? ( python_targets_python2_7 ) +SLOT=0 +SRC_URI=http://compbio.cs.toronto.edu/shrimp/releases/SHRiMP_2_2_3.src.tar.gz +_eclasses_=desktop b1d22ac8bdd4679ab79c71aca235009d epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 flag-o-matic dc34234e8c43343da45853da22dcf14b ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 1d91b03d42ab6308b5f4f6b598ed110e preserve-libs ef207dc62baddfddfd39a164d9797648 python-single-r1 36ac48e647d2627de28c87aaffb94753 python-utils-r1 611c493a4cfef5254350fabc04b606f5 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=98a7a2b9765ad5e245b1b7b9be67060b diff --git a/metadata/md5-cache/sci-biology/sibsim4-0.20 b/metadata/md5-cache/sci-biology/sibsim4-0.20 new file mode 100644 index 000000000000..77a69abaf991 --- /dev/null +++ b/metadata/md5-cache/sci-biology/sibsim4-0.20 @@ -0,0 +1,10 @@ +DEFINED_PHASES=install prepare +DESCRIPTION=A rewrite and improvement upon sim4, a DNA-mRNA aligner +EAPI=5 +HOMEPAGE=http://sibsim4.sourceforge.net/ +KEYWORDS=amd64 x86 +LICENSE=GPL-2 +SLOT=0 +SRC_URI=mirror://sourceforge/sibsim4/SIBsim4-0.20.tar.gz +_eclasses_=multilib 1d91b03d42ab6308b5f4f6b598ed110e toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c +_md5_=84a29c8972011ec4b86f3c8235a7b5d2 diff --git a/metadata/md5-cache/sci-biology/sim4-20030921-r2 b/metadata/md5-cache/sci-biology/sim4-20030921-r2 new file mode 100644 index 000000000000..2c9fee3a7db8 --- /dev/null +++ b/metadata/md5-cache/sci-biology/sim4-20030921-r2 @@ -0,0 +1,10 @@ +DEFINED_PHASES=configure install +DESCRIPTION=A program to align cDNA and genomic DNA +EAPI=7 +HOMEPAGE=http://globin.cse.psu.edu/html/docs/sim4.html +KEYWORDS=~amd64 ~ppc ~x86 +LICENSE=GPL-2 +SLOT=0 +SRC_URI=mirror://gentoo/sim4-20030921.tar.gz +_eclasses_=multilib 1d91b03d42ab6308b5f4f6b598ed110e toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c +_md5_=d9ac88a2e3ccc00187d880fcca7f5db2 diff --git a/metadata/md5-cache/sci-biology/stride-20011129-r1 b/metadata/md5-cache/sci-biology/stride-20011129-r1 new file mode 100644 index 000000000000..d2eaf4313931 --- /dev/null +++ b/metadata/md5-cache/sci-biology/stride-20011129-r1 @@ -0,0 +1,11 @@ +DEFINED_PHASES=configure install +DESCRIPTION=Protein secondary structure assignment from atomic coordinates +EAPI=7 +HOMEPAGE=http://webclu.bio.wzw.tum.de/stride/ +KEYWORDS=amd64 ppc x86 ~amd64-linux ~x86-linux ~x86-macos +LICENSE=STRIDE +RESTRICT=mirror bindist +SLOT=0 +SRC_URI=ftp://ftp.ebi.ac.uk/pub/software/unix/stride/src/stride.tar.gz -> stride-20011129.tar.gz https://dev.gentoo.org/~jlec/distfiles/stride-20060723-update.patch.bz2 +_eclasses_=multilib 1d91b03d42ab6308b5f4f6b598ed110e toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c +_md5_=897f9fd1d73b5a7779f29a7ca161cb75 diff --git a/metadata/md5-cache/sci-biology/t-coffee-11.00-r2 b/metadata/md5-cache/sci-biology/t-coffee-11.00-r2 new file mode 100644 index 000000000000..e637442ef44a --- /dev/null +++ b/metadata/md5-cache/sci-biology/t-coffee-11.00-r2 @@ -0,0 +1,11 @@ +DEFINED_PHASES=compile install prepare +DESCRIPTION=A multiple sequence alignment package +EAPI=6 +HOMEPAGE=http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html +KEYWORDS=~amd64 ~ppc ~ppc64 ~x86 ~amd64-linux ~x86-linux +LICENSE=GPL-2 +RDEPEND=sci-biology/clustalw sci-chemistry/tm-align +SLOT=0 +SRC_URI=http://www.tcoffee.org/Packages/Beta/Latest/T-COFFEE_distribution_Version_11.00.4466924.tar.gz +_eclasses_=multilib 1d91b03d42ab6308b5f4f6b598ed110e toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c +_md5_=5c54b109c5b8bef93adbc5f99ddd7114 diff --git a/metadata/md5-cache/sci-biology/tophat-2.1.1-r4 b/metadata/md5-cache/sci-biology/tophat-2.1.1-r4 new file mode 100644 index 000000000000..8632aca8b94f --- /dev/null +++ b/metadata/md5-cache/sci-biology/tophat-2.1.1-r4 @@ -0,0 +1,14 @@ +DEFINED_PHASES=configure install postinst prepare setup +DEPEND=python_single_target_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 >=dev-lang/python-exec-2:=[python_targets_python2_7] ) dev-libs/boost:=[threads] dev-python/intervaltree[python_targets_python2_7(-)?,-python_single_target_pypy3(-),-python_single_target_python3_6(-),-python_single_target_python3_7(-),-python_single_target_python3_8(-),python_single_target_python2_7(+)?] dev-python/sortedcontainers[python_targets_python2_7(-)?,-python_single_target_pypy3(-),-python_single_target_python3_6(-),-python_single_target_python3_7(-),-python_single_target_python3_8(-),python_single_target_python2_7(+)?] sci-biology/samtools:0.1-legacy sci-biology/bowtie:2 virtual/pkgconfig sci-biology/seqan:1.4 >=sys-devel/autoconf-archive-2016.09.16 >=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 +DESCRIPTION=Python-based splice junction mapper for RNA-Seq reads using bowtie2 +EAPI=6 +HOMEPAGE=https://ccb.jhu.edu/software/tophat/ +IUSE=debug +python_targets_python2_7 +python_single_target_python2_7 +KEYWORDS=~amd64 ~x86 +LICENSE=Artistic +RDEPEND=python_single_target_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 >=dev-lang/python-exec-2:=[python_targets_python2_7] ) dev-libs/boost:=[threads] dev-python/intervaltree[python_targets_python2_7(-)?,-python_single_target_pypy3(-),-python_single_target_python3_6(-),-python_single_target_python3_7(-),-python_single_target_python3_8(-),python_single_target_python2_7(+)?] dev-python/sortedcontainers[python_targets_python2_7(-)?,-python_single_target_pypy3(-),-python_single_target_python3_6(-),-python_single_target_python3_7(-),-python_single_target_python3_8(-),python_single_target_python2_7(+)?] sci-biology/samtools:0.1-legacy sci-biology/bowtie:2 +REQUIRED_USE=^^ ( python_single_target_python2_7 ) python_single_target_python2_7? ( python_targets_python2_7 ) +SLOT=0 +SRC_URI=https://ccb.jhu.edu/software/tophat/downloads/tophat-2.1.1.tar.gz +_eclasses_=autotools ea7865c8fba1ea8d3639f355fffe1a3c desktop b1d22ac8bdd4679ab79c71aca235009d epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 flag-o-matic dc34234e8c43343da45853da22dcf14b libtool f143db5a74ccd9ca28c1234deffede96 ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 1d91b03d42ab6308b5f4f6b598ed110e preserve-libs ef207dc62baddfddfd39a164d9797648 python-single-r1 36ac48e647d2627de28c87aaffb94753 python-utils-r1 611c493a4cfef5254350fabc04b606f5 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=efee8069c83c578acac8e57b429ad985 diff --git a/metadata/md5-cache/sci-biology/transfac-3.2-r1 b/metadata/md5-cache/sci-biology/transfac-3.2-r1 new file mode 100644 index 000000000000..91dec5eae8be --- /dev/null +++ b/metadata/md5-cache/sci-biology/transfac-3.2-r1 @@ -0,0 +1,12 @@ +DEFINED_PHASES=compile install +DEPEND=emboss? ( sci-biology/emboss ) +DESCRIPTION=A database of eucaryotic transcription factors +EAPI=6 +HOMEPAGE=http://www.gene-regulation.com/pub/databases.html +IUSE=emboss minimal +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux +LICENSE=public-domain +RDEPEND=emboss? ( sci-biology/emboss ) +SLOT=3 +SRC_URI=ftp://ftp.ebi.ac.uk/pub/databases/transfac/transfac32.tar.Z +_md5_=d8fcea543b5af9fc877c63800e1bd6d3 diff --git a/metadata/md5-cache/sci-biology/tree-puzzle-5.2 b/metadata/md5-cache/sci-biology/tree-puzzle-5.2 new file mode 100644 index 000000000000..a9f74c4889af --- /dev/null +++ b/metadata/md5-cache/sci-biology/tree-puzzle-5.2 @@ -0,0 +1,14 @@ +DEFINED_PHASES=configure install setup +DEPEND=mpi? ( virtual/mpi ) +DESCRIPTION=Maximum likelihood analysis for nucleotide, amino acid, and two-state data +EAPI=7 +HOMEPAGE=http://www.tree-puzzle.de +IUSE=mpi +KEYWORDS=~amd64 ~ppc x86 ~amd64-linux ~x86-linux ~ppc-macos +LICENSE=GPL-2 +RDEPEND=mpi? ( virtual/mpi ) +RESTRICT=test +SLOT=0 +SRC_URI=http://www.tree-puzzle.de/tree-puzzle-5.2.tar.gz +_eclasses_=multilib 1d91b03d42ab6308b5f4f6b598ed110e toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c +_md5_=8bd164fc83c9bb1d9a2e9559a47ff526 diff --git a/metadata/md5-cache/sci-biology/treeviewx-0.5.1-r3 b/metadata/md5-cache/sci-biology/treeviewx-0.5.1-r3 new file mode 100644 index 000000000000..2cb958fb7612 --- /dev/null +++ b/metadata/md5-cache/sci-biology/treeviewx-0.5.1-r3 @@ -0,0 +1,12 @@ +DEFINED_PHASES=prepare +DEPEND=x11-libs/wxGTK:3.0[X] >=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 +DESCRIPTION=A phylogenetic tree viewer +EAPI=5 +HOMEPAGE=http://darwin.zoology.gla.ac.uk/~rpage/treeviewx/ +KEYWORDS=amd64 x86 +LICENSE=GPL-2 +RDEPEND=x11-libs/wxGTK:3.0[X] +SLOT=0 +SRC_URI=http://darwin.zoology.gla.ac.uk/~rpage/treeviewx/download/0.5/tv-0.5.1.tar.gz +_eclasses_=autotools ea7865c8fba1ea8d3639f355fffe1a3c desktop b1d22ac8bdd4679ab79c71aca235009d epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 flag-o-matic dc34234e8c43343da45853da22dcf14b libtool f143db5a74ccd9ca28c1234deffede96 ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 1d91b03d42ab6308b5f4f6b598ed110e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf wxwidgets e1e6e1eb5b3d911b3abd712f611e2312 +_md5_=ce129f3e61a849cfd3654e5a9fa4b17a diff --git a/metadata/md5-cache/sci-biology/trf-4.04-r1 b/metadata/md5-cache/sci-biology/trf-4.04-r1 new file mode 100644 index 000000000000..3195b5c5feec --- /dev/null +++ b/metadata/md5-cache/sci-biology/trf-4.04-r1 @@ -0,0 +1,10 @@ +DEFINED_PHASES=install unpack +DESCRIPTION=Tandem Repeats Finder +EAPI=6 +HOMEPAGE=http://tandem.bu.edu/trf/trf.html +KEYWORDS=amd64 x86 +LICENSE=trf +RESTRICT=mirror bindist +SLOT=0 +SRC_URI=http://tandem.bu.edu/trf/downloads/trf404.linux +_md5_=51a51c14c6646aaa7d7494d561535729 diff --git a/metadata/md5-cache/sci-biology/trnascan-se-1.31 b/metadata/md5-cache/sci-biology/trnascan-se-1.31 new file mode 100644 index 000000000000..5e095404d113 --- /dev/null +++ b/metadata/md5-cache/sci-biology/trnascan-se-1.31 @@ -0,0 +1,10 @@ +DEFINED_PHASES=install prepare test +DESCRIPTION=tRNA detection in large-scale genome sequences +EAPI=6 +HOMEPAGE=http://lowelab.ucsc.edu/tRNAscan-SE/ +KEYWORDS=amd64 x86 +LICENSE=GPL-2 +SLOT=0 +SRC_URI=http://lowelab.ucsc.edu/software/tRNAscan-SE.tar.gz -> trnascan-se-1.31.tar.gz +_eclasses_=multilib 1d91b03d42ab6308b5f4f6b598ed110e perl-functions 6ec4c4d8fc8324200f1c14e8d158c59b toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c +_md5_=3f4bcdf31fe276f90a95e2f4b311deae diff --git a/metadata/md5-cache/sci-biology/uchime-4.2.40 b/metadata/md5-cache/sci-biology/uchime-4.2.40 new file mode 100644 index 000000000000..bc02cb9681e8 --- /dev/null +++ b/metadata/md5-cache/sci-biology/uchime-4.2.40 @@ -0,0 +1,12 @@ +DEFINED_PHASES=compile configure install prepare test +DEPEND=sys-devel/make >=dev-util/cmake-3.9.6 +DESCRIPTION=Fast, accurate chimera detection +EAPI=6 +HOMEPAGE=http://www.drive5.com/uchime/ +IUSE=debug +KEYWORDS=amd64 x86 ~amd64-linux ~x86-linux +LICENSE=public-domain +SLOT=0 +SRC_URI=http://drive5.com/uchime/uchime4.2.40_src.tar.gz +_eclasses_=cmake-utils be72eac95bd029ad1d81d5d656c3c83b desktop b1d22ac8bdd4679ab79c71aca235009d epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 flag-o-matic dc34234e8c43343da45853da22dcf14b ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 1d91b03d42ab6308b5f4f6b598ed110e multiprocessing cac3169468f893670dac3e7cb940e045 ninja-utils 132cbb376048d079b5a012f5467c4e7f preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf xdg-utils ff2ff954e6b17929574eee4efc5152ba +_md5_=6adcbb8c658bdc3c40f797c61f5c58b0 diff --git a/metadata/md5-cache/sci-biology/ucsc-genome-browser-260-r1 b/metadata/md5-cache/sci-biology/ucsc-genome-browser-260-r1 new file mode 100644 index 000000000000..5c2c5ead7d0f --- /dev/null +++ b/metadata/md5-cache/sci-biology/ucsc-genome-browser-260-r1 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile install postinst prepare prerm setup +DEPEND=dev-libs/openssl:0= media-libs/libpng:0= !<sci-biology/ucsc-genome-browser-223 mysql? ( dev-db/mysql-connector-c:0= ) server? ( virtual/httpd-cgi ) app-arch/unzip >=app-admin/webapp-config-1.50.15 +DESCRIPTION=The UCSC genome browser suite, also known as Jim Kent's library and GoldenPath +EAPI=6 +HOMEPAGE=http://genome.ucsc.edu/ +IUSE=+mysql +server static-libs vhosts +KEYWORDS=~amd64 ~x86 +LICENSE=blat +RDEPEND=dev-libs/openssl:0= media-libs/libpng:0= !<sci-biology/ucsc-genome-browser-223 mysql? ( dev-db/mysql-connector-c:0= ) server? ( virtual/httpd-cgi ) >=app-admin/webapp-config-1.50.15 +REQUIRED_USE=server? ( mysql ) +SLOT=0 +SRC_URI=http://hgdownload.cse.ucsc.edu/admin/jksrc.v260.zip +_eclasses_=desktop b1d22ac8bdd4679ab79c71aca235009d epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 flag-o-matic dc34234e8c43343da45853da22dcf14b ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 1d91b03d42ab6308b5f4f6b598ed110e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf webapp 16783e418aca3ffa461d68310bf7ab12 +_md5_=ecc35fd7ec196a9e5cce4c0c51af618f diff --git a/metadata/md5-cache/sci-biology/unafold-3.8-r1 b/metadata/md5-cache/sci-biology/unafold-3.8-r1 new file mode 100644 index 000000000000..9a19f79c0984 --- /dev/null +++ b/metadata/md5-cache/sci-biology/unafold-3.8-r1 @@ -0,0 +1,11 @@ +DEFINED_PHASES=prepare +DESCRIPTION=Unified Nucleic Acid Folding and hybridization package +EAPI=5 +HOMEPAGE=http://mfold.rna.albany.edu/ +IUSE=custom-cflags +KEYWORDS=~amd64 ~x86 +LICENSE=unafold +SLOT=0 +SRC_URI=http://dinamelt.bioinfo.rpi.edu/download/unafold-3.8.tar.bz2 +_eclasses_=desktop b1d22ac8bdd4679ab79c71aca235009d epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 flag-o-matic dc34234e8c43343da45853da22dcf14b ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 1d91b03d42ab6308b5f4f6b598ed110e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=f6e357557efc2f86eab0adadd32142ce diff --git a/metadata/md5-cache/sci-biology/update-blastdb-12.0.0 b/metadata/md5-cache/sci-biology/update-blastdb-12.0.0 new file mode 100644 index 000000000000..8541d94855d7 --- /dev/null +++ b/metadata/md5-cache/sci-biology/update-blastdb-12.0.0 @@ -0,0 +1,11 @@ +DEFINED_PHASES=install +DESCRIPTION=update_blastdb.pl for local blast db maintainance +EAPI=5 +HOMEPAGE=http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=toolkit +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux +LICENSE=public-domain +RDEPEND=dev-lang/perl !sci-biology/ncbi-tools++ +SLOT=0 +SRC_URI=ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/ARCHIVE/12_0_0/ncbi_cxx--12_0_0.tar.gz +_eclasses_=estack 686eaab303305a908fd57b2fd7617800 versionator 2352c3fc97241f6a02042773c8287748 +_md5_=bc882208706b78e231cbfd78c7b5799e diff --git a/metadata/md5-cache/sci-biology/vcftools-0.1.14 b/metadata/md5-cache/sci-biology/vcftools-0.1.14 new file mode 100644 index 000000000000..396cc560e946 --- /dev/null +++ b/metadata/md5-cache/sci-biology/vcftools-0.1.14 @@ -0,0 +1,13 @@ +DEFINED_PHASES=configure prepare +DEPEND=sys-libs/zlib dev-lang/perl:= lapack? ( virtual/lapack ) virtual/pkgconfig >=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 +DESCRIPTION=Tools for working with VCF (Variant Call Format) files +EAPI=6 +HOMEPAGE=http://vcftools.sourceforge.net/ +IUSE=lapack +KEYWORDS=~amd64 ~x86 +LICENSE=LGPL-3 +RDEPEND=sys-libs/zlib dev-lang/perl:= lapack? ( virtual/lapack ) +SLOT=0 +SRC_URI=https://github.com/vcftools/vcftools/releases/download/v0.1.14/vcftools-0.1.14.tar.gz +_eclasses_=autotools ea7865c8fba1ea8d3639f355fffe1a3c desktop b1d22ac8bdd4679ab79c71aca235009d epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 flag-o-matic dc34234e8c43343da45853da22dcf14b libtool f143db5a74ccd9ca28c1234deffede96 ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 1d91b03d42ab6308b5f4f6b598ed110e perl-functions 6ec4c4d8fc8324200f1c14e8d158c59b preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=82adffd84f2a93745e683b498b79fbe8 diff --git a/metadata/md5-cache/sci-biology/velvet-1.2.10 b/metadata/md5-cache/sci-biology/velvet-1.2.10 new file mode 100644 index 000000000000..d1244d491f3a --- /dev/null +++ b/metadata/md5-cache/sci-biology/velvet-1.2.10 @@ -0,0 +1,12 @@ +DEFINED_PHASES=compile install prepare test +DEPEND=doc? ( virtual/latex-base ) +DESCRIPTION=A sequence assembler for very short reads +EAPI=5 +HOMEPAGE=https://www.ebi.ac.uk/~zerbino/velvet/ +IUSE=doc openmp +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-2 +SLOT=0 +SRC_URI=https://www.ebi.ac.uk/~zerbino/velvet/velvet_1.2.10.tgz +_eclasses_=desktop b1d22ac8bdd4679ab79c71aca235009d epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 flag-o-matic dc34234e8c43343da45853da22dcf14b ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 1d91b03d42ab6308b5f4f6b598ed110e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=420632435bf1efe77241192fff993a20 diff --git a/metadata/md5-cache/sci-biology/vienna-rna-2.1.1 b/metadata/md5-cache/sci-biology/vienna-rna-2.1.1 new file mode 100644 index 000000000000..8279035b3268 --- /dev/null +++ b/metadata/md5-cache/sci-biology/vienna-rna-2.1.1 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile configure install prepare test unpack +DEPEND=dev-lang/perl media-libs/gd doc? ( dev-texlive/texlive-latex ) python? ( python_targets_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 ) >=dev-lang/python-exec-2:=[python_targets_python2_7(-)?,-python_single_target_python2_7(-)] ) python? ( dev-lang/swig:0 ) >=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 dev-lang/perl:=[-build(-)] +DESCRIPTION=RNA secondary structure prediction and comparison +EAPI=5 +HOMEPAGE=http://www.tbi.univie.ac.at/~ivo/RNA/ +IUSE=doc openmp python static-libs python_targets_python2_7 +KEYWORDS=amd64 ppc x86 +LICENSE=vienna-rna +RDEPEND=dev-lang/perl media-libs/gd doc? ( dev-texlive/texlive-latex ) python? ( python_targets_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 ) >=dev-lang/python-exec-2:=[python_targets_python2_7(-)?,-python_single_target_python2_7(-)] ) dev-lang/perl:=[-build(-)] +REQUIRED_USE=python? ( || ( python_targets_python2_7 ) ) +SLOT=0 +SRC_URI=http://www.tbi.univie.ac.at/~ronny/RNA/ViennaRNA-2.1.1.tar.gz +_eclasses_=autotools ea7865c8fba1ea8d3639f355fffe1a3c autotools-utils 95db0904ad0f62535e18e5ccb67cce5e desktop b1d22ac8bdd4679ab79c71aca235009d distutils-r1 c576838cd67e384002a18edd54be710e epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 libtool f143db5a74ccd9ca28c1234deffede96 ltprune 2729691420b6deeda2a90b1f1183fb55 multibuild 40fe59465edacd730c644ec2bc197809 multilib 1d91b03d42ab6308b5f4f6b598ed110e multiprocessing cac3169468f893670dac3e7cb940e045 perl-functions 6ec4c4d8fc8324200f1c14e8d158c59b perl-module 97206c028d9bdc9f248e022ac5c9fc83 preserve-libs ef207dc62baddfddfd39a164d9797648 python-r1 4eed5e0c72d4544a2291ae46515f5d79 python-utils-r1 611c493a4cfef5254350fabc04b606f5 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c unpacker 3cd8bad0d31e525cd26be1bfa4e61631 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf xdg-utils ff2ff954e6b17929574eee4efc5152ba +_md5_=1e58c830b49ced05ae9960fcc2dead13 diff --git a/metadata/md5-cache/sci-biology/vienna-rna-2.1.8 b/metadata/md5-cache/sci-biology/vienna-rna-2.1.8 new file mode 100644 index 000000000000..b8cf7b3dad0f --- /dev/null +++ b/metadata/md5-cache/sci-biology/vienna-rna-2.1.8 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile configure install prepare test unpack +DEPEND=dev-lang/perl media-libs/gd doc? ( dev-texlive/texlive-latex ) python? ( python_targets_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 ) >=dev-lang/python-exec-2:=[python_targets_python2_7(-)?,-python_single_target_python2_7(-)] ) python? ( dev-lang/swig:0 ) >=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 dev-lang/perl:=[-build(-)] +DESCRIPTION=RNA secondary structure prediction and comparison +EAPI=5 +HOMEPAGE=http://www.tbi.univie.ac.at/~ivo/RNA/ +IUSE=doc openmp python static-libs python_targets_python2_7 +KEYWORDS=~amd64 ~ppc ~x86 +LICENSE=vienna-rna +RDEPEND=dev-lang/perl media-libs/gd doc? ( dev-texlive/texlive-latex ) python? ( python_targets_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 ) >=dev-lang/python-exec-2:=[python_targets_python2_7(-)?,-python_single_target_python2_7(-)] ) dev-lang/perl:=[-build(-)] +REQUIRED_USE=python? ( || ( python_targets_python2_7 ) ) +SLOT=0 +SRC_URI=http://www.tbi.univie.ac.at/RNA/packages/source/ViennaRNA-2.1.8.tar.gz +_eclasses_=autotools ea7865c8fba1ea8d3639f355fffe1a3c autotools-utils 95db0904ad0f62535e18e5ccb67cce5e desktop b1d22ac8bdd4679ab79c71aca235009d distutils-r1 c576838cd67e384002a18edd54be710e epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 libtool f143db5a74ccd9ca28c1234deffede96 ltprune 2729691420b6deeda2a90b1f1183fb55 multibuild 40fe59465edacd730c644ec2bc197809 multilib 1d91b03d42ab6308b5f4f6b598ed110e multiprocessing cac3169468f893670dac3e7cb940e045 perl-functions 6ec4c4d8fc8324200f1c14e8d158c59b perl-module 97206c028d9bdc9f248e022ac5c9fc83 preserve-libs ef207dc62baddfddfd39a164d9797648 python-r1 4eed5e0c72d4544a2291ae46515f5d79 python-utils-r1 611c493a4cfef5254350fabc04b606f5 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c unpacker 3cd8bad0d31e525cd26be1bfa4e61631 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf xdg-utils ff2ff954e6b17929574eee4efc5152ba +_md5_=b2a6486af275e75c6365ab7eeba1e0bd diff --git a/metadata/md5-cache/sci-biology/wgs-assembler-7.0-r2 b/metadata/md5-cache/sci-biology/wgs-assembler-7.0-r2 new file mode 100644 index 000000000000..a9ee8579329e --- /dev/null +++ b/metadata/md5-cache/sci-biology/wgs-assembler-7.0-r2 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile configure install prepare +DEPEND=net-libs/libtirpc x11-libs/libXt !x11-terms/terminator +DESCRIPTION=The Celera de novo whole-genome shotgun DNA sequence assembler, aka CABOG +EAPI=6 +HOMEPAGE=https://sourceforge.net/projects/wgs-assembler/ +IUSE=static-libs +KEYWORDS=amd64 x86 +LICENSE=GPL-2 +RDEPEND=net-libs/libtirpc x11-libs/libXt !x11-terms/terminator app-shells/tcsh dev-perl/Log-Log4perl +SLOT=0 +SRC_URI=mirror://sourceforge/wgs-assembler/wgs-7.0.tar.bz2 +_eclasses_=desktop b1d22ac8bdd4679ab79c71aca235009d epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 1d91b03d42ab6308b5f4f6b598ed110e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=cb4182fc2947f2a3efa19db296a6a76f diff --git a/metadata/md5-cache/sci-biology/wise-2.4.0_alpha b/metadata/md5-cache/sci-biology/wise-2.4.0_alpha new file mode 100644 index 000000000000..a16b312dbe14 --- /dev/null +++ b/metadata/md5-cache/sci-biology/wise-2.4.0_alpha @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile install prepare test +DEPEND=~sci-biology/hmmer-2.3.2 app-shells/tcsh dev-lang/perl virtual/latex-base +DESCRIPTION=Intelligent algorithms for DNA searches +EAPI=5 +HOMEPAGE=http://www.ebi.ac.uk/Wise2/ +IUSE=doc static-libs +KEYWORDS=~amd64 ~x86 +LICENSE=BSD +RDEPEND=~sci-biology/hmmer-2.3.2 +SLOT=0 +SRC_URI=ftp://ftp.ebi.ac.uk/pub/software/wise2/wise2.4.0alpha.tar.gz https://dev.gentoo.org/~mgorny/dist/wise-2.4.0_alpha-patchset.tar.bz2 +_eclasses_=desktop b1d22ac8bdd4679ab79c71aca235009d epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 1d91b03d42ab6308b5f4f6b598ed110e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf versionator 2352c3fc97241f6a02042773c8287748 +_md5_=5089373e8fa38f080134e22ddf59264c diff --git a/metadata/md5-cache/sci-biology/yass-1.14-r2 b/metadata/md5-cache/sci-biology/yass-1.14-r2 new file mode 100644 index 000000000000..c1d9f11cfab7 --- /dev/null +++ b/metadata/md5-cache/sci-biology/yass-1.14-r2 @@ -0,0 +1,13 @@ +DEFINED_PHASES=configure prepare +DEPEND=dmalloc? ( dev-libs/dmalloc ) >=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 +DESCRIPTION=Genomic similarity search with multiple transition constrained spaced seeds +EAPI=6 +HOMEPAGE=http://bioinfo.lifl.fr/yass/ +IUSE=dmalloc lowmem threads +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-2 +RDEPEND=dmalloc? ( dev-libs/dmalloc ) +SLOT=0 +SRC_URI=http://bioinfo.lifl.fr/yass/files/yass-1.14.tar.gz +_eclasses_=autotools ea7865c8fba1ea8d3639f355fffe1a3c libtool f143db5a74ccd9ca28c1234deffede96 multilib 1d91b03d42ab6308b5f4f6b598ed110e toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c +_md5_=3a4ba9b4e7b8efec51cfc79d261fefd3 |