From e22c4c21ec9f3ee466014784de256598d26f7f28 Mon Sep 17 00:00:00 2001 From: Repository mirror & CI Date: Thu, 7 Jul 2022 20:01:43 +0000 Subject: 2022-07-07 20:01:43 UTC --- metadata/md5-cache/dev-libs/elfutils-0.187 | 4 +- metadata/md5-cache/sci-biology/amap-2.2-r4 | 14 ----- metadata/md5-cache/sci-biology/amap-2.2-r5 | 15 +++++ metadata/md5-cache/sci-biology/biogrep-1.0-r2 | 13 ----- metadata/md5-cache/sci-biology/biogrep-1.0-r3 | 13 +++++ metadata/md5-cache/sci-biology/biosql-1.0.1-r1 | 12 ---- metadata/md5-cache/sci-biology/biosql-1.0.1-r2 | 12 ++++ metadata/md5-cache/sci-biology/blat-34-r2 | 12 ---- metadata/md5-cache/sci-biology/blat-34-r3 | 12 ++++ metadata/md5-cache/sci-biology/cd-hit-4.6.6 | 13 ----- metadata/md5-cache/sci-biology/cd-hit-4.6.6-r1 | 13 +++++ metadata/md5-cache/sci-biology/clustal-omega-1.2.4 | 14 ----- .../md5-cache/sci-biology/clustal-omega-1.2.4-r1 | 14 +++++ metadata/md5-cache/sci-biology/clustalw-1.83-r4 | 6 +- metadata/md5-cache/sci-biology/clustalw-2.1-r1 | 9 --- metadata/md5-cache/sci-biology/clustalw-2.1-r2 | 9 +++ metadata/md5-cache/sci-biology/dialign2-2.2.1 | 11 ---- metadata/md5-cache/sci-biology/dialign2-2.2.1-r1 | 11 ++++ metadata/md5-cache/sci-biology/elph-1.0.1-r1 | 11 ---- metadata/md5-cache/sci-biology/elph-1.0.1-r2 | 11 ++++ metadata/md5-cache/sci-biology/embassy-6.6.0-r2 | 9 --- metadata/md5-cache/sci-biology/embassy-6.6.0-r3 | 9 +++ metadata/md5-cache/sci-biology/eugene-4.1d | 14 ----- metadata/md5-cache/sci-biology/eugene-4.1d-r1 | 15 +++++ metadata/md5-cache/sci-biology/exonerate-2.2.0-r2 | 16 ------ metadata/md5-cache/sci-biology/exonerate-2.2.0-r3 | 17 ++++++ metadata/md5-cache/sci-biology/hmmer-2.3.2-r4 | 12 ---- metadata/md5-cache/sci-biology/hmmer-2.3.2-r5 | 14 +++++ metadata/md5-cache/sci-biology/hmmer-3.1_beta2 | 13 ----- metadata/md5-cache/sci-biology/hmmer-3.1_beta2-r1 | 16 ++++++ metadata/md5-cache/sci-biology/iedera-1.05-r1 | 12 ---- metadata/md5-cache/sci-biology/iedera-1.05-r2 | 12 ++++ metadata/md5-cache/sci-biology/iqpnni-3.3.2-r1 | 10 ---- metadata/md5-cache/sci-biology/iqpnni-3.3.2-r2 | 10 ++++ metadata/md5-cache/sci-biology/kalign-2.03-r2 | 11 ---- metadata/md5-cache/sci-biology/kalign-2.03-r3 | 9 +++ metadata/md5-cache/sci-biology/maq-0.7.1-r2 | 13 ----- metadata/md5-cache/sci-biology/maq-0.7.1-r3 | 14 +++++ metadata/md5-cache/sci-biology/maqview-0.2.5-r3 | 13 ----- metadata/md5-cache/sci-biology/maqview-0.2.5-r4 | 14 +++++ metadata/md5-cache/sci-biology/mummer-3.23 | 13 ----- metadata/md5-cache/sci-biology/mummer-3.23-r1 | 13 +++++ metadata/md5-cache/sci-biology/pals-1.0-r1 | 11 ---- metadata/md5-cache/sci-biology/pals-1.0-r2 | 11 ++++ metadata/md5-cache/sci-biology/phred-071220-r1 | 12 ---- metadata/md5-cache/sci-biology/phred-071220-r2 | 12 ++++ metadata/md5-cache/sci-biology/phyml-2.4.5-r3 | 11 ---- metadata/md5-cache/sci-biology/phyml-2.4.5-r4 | 11 ++++ metadata/md5-cache/sci-biology/piler-1.0-r1 | 12 ---- metadata/md5-cache/sci-biology/piler-1.0-r2 | 12 ++++ metadata/md5-cache/sci-biology/pilercr-1.0-r1 | 11 ---- metadata/md5-cache/sci-biology/pilercr-1.0-r2 | 11 ++++ metadata/md5-cache/sci-biology/prank-140603 | 11 ---- metadata/md5-cache/sci-biology/prank-140603-r1 | 11 ++++ metadata/md5-cache/sci-biology/prodigal-2.6.3 | 11 ---- metadata/md5-cache/sci-biology/prodigal-2.6.3-r1 | 11 ++++ metadata/md5-cache/sci-biology/recon-1.08 | 13 ----- metadata/md5-cache/sci-biology/recon-1.08-r1 | 13 +++++ metadata/md5-cache/sci-biology/rnaview-20040713-r4 | 11 ---- metadata/md5-cache/sci-biology/rnaview-20040713-r5 | 11 ++++ metadata/md5-cache/sci-biology/t-coffee-11.00-r2 | 12 ---- metadata/md5-cache/sci-biology/t-coffee-11.00-r3 | 12 ++++ metadata/md5-cache/sci-biology/transfac-3.2-r1 | 12 ---- metadata/md5-cache/sci-biology/transfac-3.2-r2 | 12 ++++ metadata/md5-cache/sci-biology/trf-4.04-r1 | 10 ---- metadata/md5-cache/sci-biology/trf-4.04-r2 | 10 ++++ metadata/md5-cache/sci-biology/yass-1.14-r2 | 14 ----- metadata/md5-cache/sci-biology/yass-1.14-r3 | 15 +++++ metadata/pkg_desc_index | 64 +++++++++++----------- metadata/timestamp.chk | 2 +- profiles/use.local.desc | 2 +- 71 files changed, 444 insertions(+), 435 deletions(-) delete mode 100644 metadata/md5-cache/sci-biology/amap-2.2-r4 create mode 100644 metadata/md5-cache/sci-biology/amap-2.2-r5 delete mode 100644 metadata/md5-cache/sci-biology/biogrep-1.0-r2 create mode 100644 metadata/md5-cache/sci-biology/biogrep-1.0-r3 delete mode 100644 metadata/md5-cache/sci-biology/biosql-1.0.1-r1 create mode 100644 metadata/md5-cache/sci-biology/biosql-1.0.1-r2 delete mode 100644 metadata/md5-cache/sci-biology/blat-34-r2 create mode 100644 metadata/md5-cache/sci-biology/blat-34-r3 delete mode 100644 metadata/md5-cache/sci-biology/cd-hit-4.6.6 create mode 100644 metadata/md5-cache/sci-biology/cd-hit-4.6.6-r1 delete mode 100644 metadata/md5-cache/sci-biology/clustal-omega-1.2.4 create mode 100644 metadata/md5-cache/sci-biology/clustal-omega-1.2.4-r1 delete mode 100644 metadata/md5-cache/sci-biology/clustalw-2.1-r1 create mode 100644 metadata/md5-cache/sci-biology/clustalw-2.1-r2 delete mode 100644 metadata/md5-cache/sci-biology/dialign2-2.2.1 create mode 100644 metadata/md5-cache/sci-biology/dialign2-2.2.1-r1 delete mode 100644 metadata/md5-cache/sci-biology/elph-1.0.1-r1 create mode 100644 metadata/md5-cache/sci-biology/elph-1.0.1-r2 delete mode 100644 metadata/md5-cache/sci-biology/embassy-6.6.0-r2 create mode 100644 metadata/md5-cache/sci-biology/embassy-6.6.0-r3 delete mode 100644 metadata/md5-cache/sci-biology/eugene-4.1d create mode 100644 metadata/md5-cache/sci-biology/eugene-4.1d-r1 delete mode 100644 metadata/md5-cache/sci-biology/exonerate-2.2.0-r2 create mode 100644 metadata/md5-cache/sci-biology/exonerate-2.2.0-r3 delete mode 100644 metadata/md5-cache/sci-biology/hmmer-2.3.2-r4 create mode 100644 metadata/md5-cache/sci-biology/hmmer-2.3.2-r5 delete mode 100644 metadata/md5-cache/sci-biology/hmmer-3.1_beta2 create mode 100644 metadata/md5-cache/sci-biology/hmmer-3.1_beta2-r1 delete mode 100644 metadata/md5-cache/sci-biology/iedera-1.05-r1 create mode 100644 metadata/md5-cache/sci-biology/iedera-1.05-r2 delete mode 100644 metadata/md5-cache/sci-biology/iqpnni-3.3.2-r1 create mode 100644 metadata/md5-cache/sci-biology/iqpnni-3.3.2-r2 delete mode 100644 metadata/md5-cache/sci-biology/kalign-2.03-r2 create mode 100644 metadata/md5-cache/sci-biology/kalign-2.03-r3 delete mode 100644 metadata/md5-cache/sci-biology/maq-0.7.1-r2 create mode 100644 metadata/md5-cache/sci-biology/maq-0.7.1-r3 delete mode 100644 metadata/md5-cache/sci-biology/maqview-0.2.5-r3 create mode 100644 metadata/md5-cache/sci-biology/maqview-0.2.5-r4 delete mode 100644 metadata/md5-cache/sci-biology/mummer-3.23 create mode 100644 metadata/md5-cache/sci-biology/mummer-3.23-r1 delete mode 100644 metadata/md5-cache/sci-biology/pals-1.0-r1 create mode 100644 metadata/md5-cache/sci-biology/pals-1.0-r2 delete mode 100644 metadata/md5-cache/sci-biology/phred-071220-r1 create mode 100644 metadata/md5-cache/sci-biology/phred-071220-r2 delete mode 100644 metadata/md5-cache/sci-biology/phyml-2.4.5-r3 create mode 100644 metadata/md5-cache/sci-biology/phyml-2.4.5-r4 delete mode 100644 metadata/md5-cache/sci-biology/piler-1.0-r1 create mode 100644 metadata/md5-cache/sci-biology/piler-1.0-r2 delete mode 100644 metadata/md5-cache/sci-biology/pilercr-1.0-r1 create mode 100644 metadata/md5-cache/sci-biology/pilercr-1.0-r2 delete mode 100644 metadata/md5-cache/sci-biology/prank-140603 create mode 100644 metadata/md5-cache/sci-biology/prank-140603-r1 delete mode 100644 metadata/md5-cache/sci-biology/prodigal-2.6.3 create mode 100644 metadata/md5-cache/sci-biology/prodigal-2.6.3-r1 delete mode 100644 metadata/md5-cache/sci-biology/recon-1.08 create mode 100644 metadata/md5-cache/sci-biology/recon-1.08-r1 delete mode 100644 metadata/md5-cache/sci-biology/rnaview-20040713-r4 create mode 100644 metadata/md5-cache/sci-biology/rnaview-20040713-r5 delete mode 100644 metadata/md5-cache/sci-biology/t-coffee-11.00-r2 create mode 100644 metadata/md5-cache/sci-biology/t-coffee-11.00-r3 delete mode 100644 metadata/md5-cache/sci-biology/transfac-3.2-r1 create mode 100644 metadata/md5-cache/sci-biology/transfac-3.2-r2 delete mode 100644 metadata/md5-cache/sci-biology/trf-4.04-r1 create mode 100644 metadata/md5-cache/sci-biology/trf-4.04-r2 delete mode 100644 metadata/md5-cache/sci-biology/yass-1.14-r2 create mode 100644 metadata/md5-cache/sci-biology/yass-1.14-r3 diff --git a/metadata/md5-cache/dev-libs/elfutils-0.187 b/metadata/md5-cache/dev-libs/elfutils-0.187 index adcd11210554..85272ed14548 100644 --- a/metadata/md5-cache/dev-libs/elfutils-0.187 +++ b/metadata/md5-cache/dev-libs/elfutils-0.187 @@ -6,11 +6,11 @@ EAPI=7 HOMEPAGE=https://sourceware.org/elfutils/ INHERIT=flag-o-matic multilib-minimal verify-sig IUSE=bzip2 lzma nls static-libs test +threads +utils valgrind zstd abi_x86_32 abi_x86_64 abi_x86_x32 abi_mips_n32 abi_mips_n64 abi_mips_o32 abi_s390_32 abi_s390_64 verify-sig -KEYWORDS=~alpha amd64 arm arm64 ~hppa ~ia64 ~loong ~m68k ~mips ppc ppc64 ~riscv ~s390 sparc x86 ~amd64-linux ~x86-linux +KEYWORDS=~alpha amd64 arm arm64 hppa ~ia64 ~loong ~m68k ~mips ppc ppc64 ~riscv ~s390 sparc x86 ~amd64-linux ~x86-linux LICENSE=|| ( GPL-2+ LGPL-3+ ) utils? ( GPL-3+ ) RDEPEND=>=sys-libs/zlib-1.2.8-r1[static-libs?,abi_x86_32(-)?,abi_x86_64(-)?,abi_x86_x32(-)?,abi_mips_n32(-)?,abi_mips_n64(-)?,abi_mips_o32(-)?,abi_s390_32(-)?,abi_s390_64(-)?] bzip2? ( >=app-arch/bzip2-1.0.6-r4[static-libs?,abi_x86_32(-)?,abi_x86_64(-)?,abi_x86_x32(-)?,abi_mips_n32(-)?,abi_mips_n64(-)?,abi_mips_o32(-)?,abi_s390_32(-)?,abi_s390_64(-)?] ) lzma? ( >=app-arch/xz-utils-5.0.5-r1[static-libs?,abi_x86_32(-)?,abi_x86_64(-)?,abi_x86_x32(-)?,abi_mips_n32(-)?,abi_mips_n64(-)?,abi_mips_o32(-)?,abi_s390_32(-)?,abi_s390_64(-)?] ) zstd? ( app-arch/zstd:=[static-libs?,abi_x86_32(-)?,abi_x86_64(-)?,abi_x86_x32(-)?,abi_mips_n32(-)?,abi_mips_n64(-)?,abi_mips_o32(-)?,abi_s390_32(-)?,abi_s390_64(-)?] ) elibc_musl? ( dev-libs/libbsd sys-libs/argp-standalone sys-libs/fts-standalone sys-libs/obstack-standalone ) !dev-libs/libelf RESTRICT=!test? ( test ) SLOT=0 SRC_URI=https://sourceware.org/elfutils/ftp/0.187/elfutils-0.187.tar.bz2 https://dev.gentoo.org/~sam/distfiles/dev-libs/elfutils/elfutils-0.187-patches.tar.xz verify-sig? ( https://sourceware.org/elfutils/ftp/0.187/elfutils-0.187.tar.bz2.sig ) _eclasses_=toolchain-funcs e9da88162e7a3c60376e80c2c2adcdfb multilib 4fbbbc98f236f1b43acd99476bc3cd85 edos2unix 33e347e171066657f91f8b0c72ec8773 strip-linguas ac3ee41ee2d31d8c41a77c0838320cc7 wrapper 4a1902f969e5718126434fc35f3a0d9c eutils dab5d8ec471d025b79c9e6906bcf3bff flag-o-matic a3abd6002fafb3022597be6b8d01f88b multibuild d26d81f242cb193d899a72bca423d0bd multilib-build 05f207909a804c9174bc39a00547d598 multilib-minimal 4b0f1857965db8869a729948d5277e0b verify-sig 0748d665fa664a87add00152ed046e16 -_md5_=c5515fc12405c89406fa77beaf33266f +_md5_=4e68bde88ded9e37c4377e1b09d3c9bd diff --git a/metadata/md5-cache/sci-biology/amap-2.2-r4 b/metadata/md5-cache/sci-biology/amap-2.2-r4 deleted file mode 100644 index 6fe604cd8644..000000000000 --- a/metadata/md5-cache/sci-biology/amap-2.2-r4 +++ /dev/null @@ -1,14 +0,0 @@ -DEFINED_PHASES=compile configure install preinst prepare setup -DEPEND=java? ( >=virtual/jdk-1.8:* ) java? ( >=dev-java/java-config-2.2.0-r3 ) java? ( >=dev-java/ant-core-1.8.2:0 dev-java/javatoolkit ) -DESCRIPTION=Protein multiple-alignment-based sequence annealing -EAPI=6 -HOMEPAGE=https://wiki.gentoo.org/wiki/No_homepage -INHERIT=java-pkg-opt-2 java-ant-2 toolchain-funcs -IUSE=java java -KEYWORDS=~amd64 ~x86 -LICENSE=GPL-2 -RDEPEND=java? ( >=virtual/jre-1.8:* ) 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_=eapi7-ver 1a0a60ad07c8b32d2faba2d085dc0f24 desktop 22952d8f27cac191d75529d4c38e6bfa edos2unix 33e347e171066657f91f8b0c72ec8773 estack 055c42df72f76a4f45ec92b35e83cd56 epatch 28f0f3c0226306ec5f49e13bf851f171 toolchain-funcs e9da88162e7a3c60376e80c2c2adcdfb multilib 4fbbbc98f236f1b43acd99476bc3cd85 ltprune 97143780d341cc8d8f1d4c6187a36d29 preserve-libs a8e50acee31b5759b4df1f7707cae54b strip-linguas ac3ee41ee2d31d8c41a77c0838320cc7 vcs-clean d271b7bc7e6a009758d7d4ef749174e3 wrapper 4a1902f969e5718126434fc35f3a0d9c eutils dab5d8ec471d025b79c9e6906bcf3bff versionator d3fb3ba33acc3bbbdc4d7970227c100d java-utils-2 c0a9bd68d938ab2d3a7e237fd05f1dd8 java-pkg-opt-2 a71433e535af8faae0c0f6c861a32054 java-ant-2 5cf479aa9e0ac9cc55899f2762c2aaa0 -_md5_=857434504156a8892f1335babe24f9f0 diff --git a/metadata/md5-cache/sci-biology/amap-2.2-r5 b/metadata/md5-cache/sci-biology/amap-2.2-r5 new file mode 100644 index 000000000000..d385d6ddf32b --- /dev/null +++ b/metadata/md5-cache/sci-biology/amap-2.2-r5 @@ -0,0 +1,15 @@ +BDEPEND=java? ( >=virtual/jre-1.8:* ) +DEFINED_PHASES=compile configure install preinst prepare setup +DEPEND=java? ( >=dev-java/java-config-2.2.0-r3 ) java? ( >=dev-java/ant-core-1.8.2:0 dev-java/javatoolkit ) +DESCRIPTION=Protein multiple-alignment-based sequence annealing +EAPI=8 +HOMEPAGE=https://wiki.gentoo.org/wiki/No_homepage +INHERIT=java-pkg-opt-2 java-ant-2 toolchain-funcs +IUSE=java java +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-2 +RDEPEND=java? ( >=virtual/jre-1.8:* ) 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_=java-utils-2 c0a9bd68d938ab2d3a7e237fd05f1dd8 java-pkg-opt-2 a71433e535af8faae0c0f6c861a32054 multilib 4fbbbc98f236f1b43acd99476bc3cd85 toolchain-funcs e9da88162e7a3c60376e80c2c2adcdfb java-ant-2 5cf479aa9e0ac9cc55899f2762c2aaa0 +_md5_=b4e132581d5e91612a875f7f94387a1b diff --git a/metadata/md5-cache/sci-biology/biogrep-1.0-r2 b/metadata/md5-cache/sci-biology/biogrep-1.0-r2 deleted file mode 100644 index 9ad90512342e..000000000000 --- a/metadata/md5-cache/sci-biology/biogrep-1.0-r2 +++ /dev/null @@ -1,13 +0,0 @@ -DEFINED_PHASES=install prepare -DEPEND=sys-devel/gnuconfig >=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.5:1.16 ) >=sys-devel/autoconf-2.71 >=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 -INHERIT=autotools -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_=desktop 22952d8f27cac191d75529d4c38e6bfa edos2unix 33e347e171066657f91f8b0c72ec8773 estack 055c42df72f76a4f45ec92b35e83cd56 epatch 28f0f3c0226306ec5f49e13bf851f171 toolchain-funcs e9da88162e7a3c60376e80c2c2adcdfb multilib 4fbbbc98f236f1b43acd99476bc3cd85 ltprune 97143780d341cc8d8f1d4c6187a36d29 preserve-libs a8e50acee31b5759b4df1f7707cae54b strip-linguas ac3ee41ee2d31d8c41a77c0838320cc7 vcs-clean d271b7bc7e6a009758d7d4ef749174e3 wrapper 4a1902f969e5718126434fc35f3a0d9c eutils dab5d8ec471d025b79c9e6906bcf3bff gnuconfig b6b3e92f8b8c996400074b5f61a59256 libtool 241a8f577b9781a42a7421e53448a44e autotools 2fd69a56a527d12409ba43c733b7ac8f -_md5_=9731727dae2a2514bcaa486b0059272e diff --git a/metadata/md5-cache/sci-biology/biogrep-1.0-r3 b/metadata/md5-cache/sci-biology/biogrep-1.0-r3 new file mode 100644 index 000000000000..e1299a619479 --- /dev/null +++ b/metadata/md5-cache/sci-biology/biogrep-1.0-r3 @@ -0,0 +1,13 @@ +BDEPEND=sys-devel/gnuconfig >=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.5:1.16 ) >=sys-devel/autoconf-2.71 >=sys-devel/libtool-2.4 +DEFINED_PHASES=install prepare +DESCRIPTION=Multithreaded tool for matching large sets of patterns against biosequence DBs +EAPI=8 +HOMEPAGE=http://stephanopoulos.openwetware.org/BIOGREP.html +INHERIT=autotools +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_=gnuconfig b6b3e92f8b8c996400074b5f61a59256 toolchain-funcs e9da88162e7a3c60376e80c2c2adcdfb multilib 4fbbbc98f236f1b43acd99476bc3cd85 libtool 241a8f577b9781a42a7421e53448a44e autotools 2fd69a56a527d12409ba43c733b7ac8f +_md5_=18fc653ace8feaf53e4d1c1818b7b00c diff --git a/metadata/md5-cache/sci-biology/biosql-1.0.1-r1 b/metadata/md5-cache/sci-biology/biosql-1.0.1-r1 deleted file mode 100644 index 2a7fa17d9aa9..000000000000 --- a/metadata/md5-cache/sci-biology/biosql-1.0.1-r1 +++ /dev/null @@ -1,12 +0,0 @@ -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/biosql-1.0.1-r2 b/metadata/md5-cache/sci-biology/biosql-1.0.1-r2 new file mode 100644 index 000000000000..54c0036aa974 --- /dev/null +++ b/metadata/md5-cache/sci-biology/biosql-1.0.1-r2 @@ -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=8 +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_=6438fefd6b37886a8a237f7e9b0c1258 diff --git a/metadata/md5-cache/sci-biology/blat-34-r2 b/metadata/md5-cache/sci-biology/blat-34-r2 deleted file mode 100644 index b4f51041763c..000000000000 --- a/metadata/md5-cache/sci-biology/blat-34-r2 +++ /dev/null @@ -1,12 +0,0 @@ -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/ -INHERIT=toolchain-funcs -KEYWORDS=~amd64 ~x86 -LICENSE=blat -SLOT=0 -SRC_URI=http://www.soe.ucsc.edu/~kent/src/blatSrc34.zip -_eclasses_=toolchain-funcs e9da88162e7a3c60376e80c2c2adcdfb multilib 4fbbbc98f236f1b43acd99476bc3cd85 -_md5_=9fb0b819fe1d2fa16c86c748d885fc84 diff --git a/metadata/md5-cache/sci-biology/blat-34-r3 b/metadata/md5-cache/sci-biology/blat-34-r3 new file mode 100644 index 000000000000..9a84ea37c00a --- /dev/null +++ b/metadata/md5-cache/sci-biology/blat-34-r3 @@ -0,0 +1,12 @@ +BDEPEND=app-arch/unzip +DEFINED_PHASES=compile install +DESCRIPTION=The BLAST-Like Alignment Tool, a fast genomic sequence aligner +EAPI=8 +HOMEPAGE=http://www.cse.ucsc.edu/~kent/ +INHERIT=toolchain-funcs +KEYWORDS=~amd64 ~x86 +LICENSE=blat +SLOT=0 +SRC_URI=http://www.soe.ucsc.edu/~kent/src/blatSrc34.zip +_eclasses_=toolchain-funcs e9da88162e7a3c60376e80c2c2adcdfb multilib 4fbbbc98f236f1b43acd99476bc3cd85 +_md5_=5de19b6facdbdd7214fad082a7d27f77 diff --git a/metadata/md5-cache/sci-biology/cd-hit-4.6.6 b/metadata/md5-cache/sci-biology/cd-hit-4.6.6 deleted file mode 100644 index 30cb1cb555c3..000000000000 --- a/metadata/md5-cache/sci-biology/cd-hit-4.6.6 +++ /dev/null @@ -1,13 +0,0 @@ -DEFINED_PHASES=compile install pretend setup -DESCRIPTION=Clustering Database at High Identity with Tolerance -EAPI=6 -HOMEPAGE=http://weizhong-lab.ucsd.edu/cd-hit/ -INHERIT=flag-o-matic toolchain-funcs -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_=toolchain-funcs e9da88162e7a3c60376e80c2c2adcdfb multilib 4fbbbc98f236f1b43acd99476bc3cd85 desktop 22952d8f27cac191d75529d4c38e6bfa edos2unix 33e347e171066657f91f8b0c72ec8773 estack 055c42df72f76a4f45ec92b35e83cd56 epatch 28f0f3c0226306ec5f49e13bf851f171 ltprune 97143780d341cc8d8f1d4c6187a36d29 preserve-libs a8e50acee31b5759b4df1f7707cae54b strip-linguas ac3ee41ee2d31d8c41a77c0838320cc7 vcs-clean d271b7bc7e6a009758d7d4ef749174e3 wrapper 4a1902f969e5718126434fc35f3a0d9c eutils dab5d8ec471d025b79c9e6906bcf3bff flag-o-matic a3abd6002fafb3022597be6b8d01f88b -_md5_=bbe0ae10275a73485487e08f19f4ac1b diff --git a/metadata/md5-cache/sci-biology/cd-hit-4.6.6-r1 b/metadata/md5-cache/sci-biology/cd-hit-4.6.6-r1 new file mode 100644 index 000000000000..d8bed9e4e35f --- /dev/null +++ b/metadata/md5-cache/sci-biology/cd-hit-4.6.6-r1 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile install pretend setup +DESCRIPTION=Clustering Database at High Identity with Tolerance +EAPI=8 +HOMEPAGE=http://weizhong-lab.ucsd.edu/cd-hit/ +INHERIT=toolchain-funcs +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_=toolchain-funcs e9da88162e7a3c60376e80c2c2adcdfb multilib 4fbbbc98f236f1b43acd99476bc3cd85 +_md5_=72c254d2d4b43c49ff9b0ddcde699acb diff --git a/metadata/md5-cache/sci-biology/clustal-omega-1.2.4 b/metadata/md5-cache/sci-biology/clustal-omega-1.2.4 deleted file mode 100644 index d57a4ed38777..000000000000 --- a/metadata/md5-cache/sci-biology/clustal-omega-1.2.4 +++ /dev/null @@ -1,14 +0,0 @@ -DEFINED_PHASES=configure install prepare -DEPEND=dev-libs/argtable sys-devel/gnuconfig >=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.5:1.16 ) >=sys-devel/autoconf-2.71 >=sys-devel/libtool-2.4 -DESCRIPTION=Scalable multiple alignment of protein sequences -EAPI=6 -HOMEPAGE=http://www.clustal.org/omega/ -INHERIT=autotools -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_=desktop 22952d8f27cac191d75529d4c38e6bfa edos2unix 33e347e171066657f91f8b0c72ec8773 estack 055c42df72f76a4f45ec92b35e83cd56 epatch 28f0f3c0226306ec5f49e13bf851f171 toolchain-funcs e9da88162e7a3c60376e80c2c2adcdfb multilib 4fbbbc98f236f1b43acd99476bc3cd85 ltprune 97143780d341cc8d8f1d4c6187a36d29 preserve-libs a8e50acee31b5759b4df1f7707cae54b strip-linguas ac3ee41ee2d31d8c41a77c0838320cc7 vcs-clean d271b7bc7e6a009758d7d4ef749174e3 wrapper 4a1902f969e5718126434fc35f3a0d9c eutils dab5d8ec471d025b79c9e6906bcf3bff gnuconfig b6b3e92f8b8c996400074b5f61a59256 libtool 241a8f577b9781a42a7421e53448a44e autotools 2fd69a56a527d12409ba43c733b7ac8f -_md5_=9ade45d2e283bc5fcc7eef16725e18ae diff --git a/metadata/md5-cache/sci-biology/clustal-omega-1.2.4-r1 b/metadata/md5-cache/sci-biology/clustal-omega-1.2.4-r1 new file mode 100644 index 000000000000..66f168f721e6 --- /dev/null +++ b/metadata/md5-cache/sci-biology/clustal-omega-1.2.4-r1 @@ -0,0 +1,14 @@ +BDEPEND=sys-devel/gnuconfig >=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.5:1.16 ) >=sys-devel/autoconf-2.71 >=sys-devel/libtool-2.4 +DEFINED_PHASES=install prepare +DEPEND=dev-libs/argtable +DESCRIPTION=Scalable multiple alignment of protein sequences +EAPI=8 +HOMEPAGE=http://www.clustal.org/omega/ +INHERIT=autotools +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_=gnuconfig b6b3e92f8b8c996400074b5f61a59256 toolchain-funcs e9da88162e7a3c60376e80c2c2adcdfb multilib 4fbbbc98f236f1b43acd99476bc3cd85 libtool 241a8f577b9781a42a7421e53448a44e autotools 2fd69a56a527d12409ba43c733b7ac8f +_md5_=1fe31c7bf68a0e3d5cd862d476a40e5b diff --git a/metadata/md5-cache/sci-biology/clustalw-1.83-r4 b/metadata/md5-cache/sci-biology/clustalw-1.83-r4 index b5761bb416cf..da4310694795 100644 --- a/metadata/md5-cache/sci-biology/clustalw-1.83-r4 +++ b/metadata/md5-cache/sci-biology/clustalw-1.83-r4 @@ -1,6 +1,6 @@ -DEFINED_PHASES=install prepare +DEFINED_PHASES=configure install prepare DESCRIPTION=General purpose multiple alignment program for DNA and proteins -EAPI=6 +EAPI=8 HOMEPAGE=http://www.embl-heidelberg.de/~seqanal/ INHERIT=toolchain-funcs KEYWORDS=amd64 ~ppc ppc64 sparc x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris @@ -8,4 +8,4 @@ LICENSE=clustalw SLOT=1 SRC_URI=ftp://ftp.ebi.ac.uk/pub/software/unix/clustalw/clustalw1.83.UNIX.tar.gz _eclasses_=toolchain-funcs e9da88162e7a3c60376e80c2c2adcdfb multilib 4fbbbc98f236f1b43acd99476bc3cd85 -_md5_=0bc3b2f2f4e07f1d81ee076b0fbe6c60 +_md5_=ddae5c7662955525ce9e2a946d0d953c diff --git a/metadata/md5-cache/sci-biology/clustalw-2.1-r1 b/metadata/md5-cache/sci-biology/clustalw-2.1-r1 deleted file mode 100644 index 4efa2f629660..000000000000 --- a/metadata/md5-cache/sci-biology/clustalw-2.1-r1 +++ /dev/null @@ -1,9 +0,0 @@ -DEFINED_PHASES=install -DESCRIPTION=General purpose multiple alignment program for DNA and proteins -EAPI=6 -HOMEPAGE=http://www.clustal.org/ -KEYWORDS=amd64 ~ppc ~ppc64 ~sparc 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_=c164ea7c4a56d9c6619a6d13320cb5bd diff --git a/metadata/md5-cache/sci-biology/clustalw-2.1-r2 b/metadata/md5-cache/sci-biology/clustalw-2.1-r2 new file mode 100644 index 000000000000..7b122c7fd0d2 --- /dev/null +++ b/metadata/md5-cache/sci-biology/clustalw-2.1-r2 @@ -0,0 +1,9 @@ +DEFINED_PHASES=install +DESCRIPTION=General purpose multiple alignment program for DNA and proteins +EAPI=8 +HOMEPAGE=http://www.clustal.org/ +KEYWORDS=amd64 ~ppc ~ppc64 ~sparc 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_=41f8e585e292038a668776536cc42cb8 diff --git a/metadata/md5-cache/sci-biology/dialign2-2.2.1 b/metadata/md5-cache/sci-biology/dialign2-2.2.1 deleted file mode 100644 index c680067861d2..000000000000 --- a/metadata/md5-cache/sci-biology/dialign2-2.2.1 +++ /dev/null @@ -1,11 +0,0 @@ -DEFINED_PHASES=compile configure install -DESCRIPTION=Multiple sequence alignment -EAPI=6 -HOMEPAGE=http://bibiserv.techfak.uni-bielefeld.de/dialign -INHERIT=flag-o-matic toolchain-funcs -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_=toolchain-funcs e9da88162e7a3c60376e80c2c2adcdfb multilib 4fbbbc98f236f1b43acd99476bc3cd85 desktop 22952d8f27cac191d75529d4c38e6bfa edos2unix 33e347e171066657f91f8b0c72ec8773 estack 055c42df72f76a4f45ec92b35e83cd56 epatch 28f0f3c0226306ec5f49e13bf851f171 ltprune 97143780d341cc8d8f1d4c6187a36d29 preserve-libs a8e50acee31b5759b4df1f7707cae54b strip-linguas ac3ee41ee2d31d8c41a77c0838320cc7 vcs-clean d271b7bc7e6a009758d7d4ef749174e3 wrapper 4a1902f969e5718126434fc35f3a0d9c eutils dab5d8ec471d025b79c9e6906bcf3bff flag-o-matic a3abd6002fafb3022597be6b8d01f88b -_md5_=3761a69a47f38308f54ae0b051361ed6 diff --git a/metadata/md5-cache/sci-biology/dialign2-2.2.1-r1 b/metadata/md5-cache/sci-biology/dialign2-2.2.1-r1 new file mode 100644 index 000000000000..343aabfb8cbe --- /dev/null +++ b/metadata/md5-cache/sci-biology/dialign2-2.2.1-r1 @@ -0,0 +1,11 @@ +DEFINED_PHASES=compile configure install +DESCRIPTION=Multiple sequence alignment +EAPI=8 +HOMEPAGE=http://bibiserv.techfak.uni-bielefeld.de/dialign +INHERIT=toolchain-funcs +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_=toolchain-funcs e9da88162e7a3c60376e80c2c2adcdfb multilib 4fbbbc98f236f1b43acd99476bc3cd85 +_md5_=879353dc71e4dca1cd8026068a0c808c diff --git a/metadata/md5-cache/sci-biology/elph-1.0.1-r1 b/metadata/md5-cache/sci-biology/elph-1.0.1-r1 deleted file mode 100644 index 35839f43cfe4..000000000000 --- a/metadata/md5-cache/sci-biology/elph-1.0.1-r1 +++ /dev/null @@ -1,11 +0,0 @@ -DEFINED_PHASES=configure install -DESCRIPTION=Estimated Locations of Pattern Hits - Motif finder program -EAPI=6 -HOMEPAGE=http://cbcb.umd.edu/software/ELPH/ -INHERIT=toolchain-funcs -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_=toolchain-funcs e9da88162e7a3c60376e80c2c2adcdfb multilib 4fbbbc98f236f1b43acd99476bc3cd85 -_md5_=dbee2f511488caf9eadadb20d043a2da diff --git a/metadata/md5-cache/sci-biology/elph-1.0.1-r2 b/metadata/md5-cache/sci-biology/elph-1.0.1-r2 new file mode 100644 index 000000000000..2242e048acd4 --- /dev/null +++ b/metadata/md5-cache/sci-biology/elph-1.0.1-r2 @@ -0,0 +1,11 @@ +DEFINED_PHASES=configure install +DESCRIPTION=Estimated Locations of Pattern Hits - Motif finder program +EAPI=8 +HOMEPAGE=http://cbcb.umd.edu/software/ELPH/ +INHERIT=toolchain-funcs +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_=toolchain-funcs e9da88162e7a3c60376e80c2c2adcdfb multilib 4fbbbc98f236f1b43acd99476bc3cd85 +_md5_=12ec147b7c0b74b6a61b6fb56542afb5 diff --git a/metadata/md5-cache/sci-biology/embassy-6.6.0-r2 b/metadata/md5-cache/sci-biology/embassy-6.6.0-r2 deleted file mode 100644 index da79487711b8..000000000000 --- a/metadata/md5-cache/sci-biology/embassy-6.6.0-r2 +++ /dev/null @@ -1,9 +0,0 @@ -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-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_=f0bb78193b5ac077edf12dbcf43e4eb2 diff --git a/metadata/md5-cache/sci-biology/embassy-6.6.0-r3 b/metadata/md5-cache/sci-biology/embassy-6.6.0-r3 new file mode 100644 index 000000000000..0e21d758fe16 --- /dev/null +++ b/metadata/md5-cache/sci-biology/embassy-6.6.0-r3 @@ -0,0 +1,9 @@ +DEFINED_PHASES=- +DESCRIPTION=A meta-package for installing all EMBASSY packages (EMBOSS add-ons) +EAPI=8 +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-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_=333771824b2ddf2c69b9e8dbf988bfd9 diff --git a/metadata/md5-cache/sci-biology/eugene-4.1d b/metadata/md5-cache/sci-biology/eugene-4.1d deleted file mode 100644 index b803299b82d3..000000000000 --- a/metadata/md5-cache/sci-biology/eugene-4.1d +++ /dev/null @@ -1,14 +0,0 @@ -DEFINED_PHASES=prepare -DEPEND=media-libs/gd[png] media-libs/libpng:0= sys-devel/gnuconfig >=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.5:1.16 ) >=sys-devel/autoconf-2.71 >=sys-devel/libtool-2.4 -DESCRIPTION=Prokaryotic and Eukaryotic gene predictor -EAPI=6 -HOMEPAGE=http://eugene.toulouse.inra.fr/ -INHERIT=autotools -KEYWORDS=amd64 x86 -LICENSE=Artistic -RDEPEND=media-libs/gd[png] media-libs/libpng:0= -RESTRICT=test -SLOT=0 -SRC_URI=https://mulcyber.toulouse.inra.fr/frs/download.php/1359/eugene-4.1d.tar.gz -_eclasses_=desktop 22952d8f27cac191d75529d4c38e6bfa edos2unix 33e347e171066657f91f8b0c72ec8773 estack 055c42df72f76a4f45ec92b35e83cd56 epatch 28f0f3c0226306ec5f49e13bf851f171 toolchain-funcs e9da88162e7a3c60376e80c2c2adcdfb multilib 4fbbbc98f236f1b43acd99476bc3cd85 ltprune 97143780d341cc8d8f1d4c6187a36d29 preserve-libs a8e50acee31b5759b4df1f7707cae54b strip-linguas ac3ee41ee2d31d8c41a77c0838320cc7 vcs-clean d271b7bc7e6a009758d7d4ef749174e3 wrapper 4a1902f969e5718126434fc35f3a0d9c eutils dab5d8ec471d025b79c9e6906bcf3bff gnuconfig b6b3e92f8b8c996400074b5f61a59256 libtool 241a8f577b9781a42a7421e53448a44e autotools 2fd69a56a527d12409ba43c733b7ac8f -_md5_=683d1e7f9daeda6cd20b92117330ea81 diff --git a/metadata/md5-cache/sci-biology/eugene-4.1d-r1 b/metadata/md5-cache/sci-biology/eugene-4.1d-r1 new file mode 100644 index 000000000000..c4eacaad659a --- /dev/null +++ b/metadata/md5-cache/sci-biology/eugene-4.1d-r1 @@ -0,0 +1,15 @@ +BDEPEND=sys-devel/gnuconfig >=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.5:1.16 ) >=sys-devel/autoconf-2.71 >=sys-devel/libtool-2.4 +DEFINED_PHASES=prepare +DEPEND=media-libs/gd[png] media-libs/libpng:= 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+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_=gnuconfig b6b3e92f8b8c996400074b5f61a59256 toolchain-funcs e9da88162e7a3c60376e80c2c2adcdfb multilib 4fbbbc98f236f1b43acd99476bc3cd85 libtool 241a8f577b9781a42a7421e53448a44e autotools 2fd69a56a527d12409ba43c733b7ac8f +_md5_=063e8f4add19e5b685018dfb11be0196 diff --git a/metadata/md5-cache/sci-biology/maqview-0.2.5-r3 b/metadata/md5-cache/sci-biology/maqview-0.2.5-r3 deleted file mode 100644 index 784bcd8d4fb5..000000000000 --- a/metadata/md5-cache/sci-biology/maqview-0.2.5-r3 +++ /dev/null @@ -1,13 +0,0 @@ -DEFINED_PHASES=prepare -DEPEND=media-libs/freeglut sys-libs/zlib sys-devel/gnuconfig >=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.5:1.16 ) >=sys-devel/autoconf-2.71 >=sys-devel/libtool-2.4 -DESCRIPTION=GUI for sci-biology/maq, a short read mapping assembler -EAPI=6 -HOMEPAGE=http://maq.sourceforge.net/ -INHERIT=autotools 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000000000000..bde5913098ec --- /dev/null +++ b/metadata/md5-cache/sci-biology/maqview-0.2.5-r4 @@ -0,0 +1,14 @@ +BDEPEND=sys-devel/gnuconfig >=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.5:1.16 ) >=sys-devel/autoconf-2.71 >=sys-devel/libtool-2.4 +DEFINED_PHASES=prepare +DEPEND=media-libs/freeglut sys-libs/zlib +DESCRIPTION=GUI for sci-biology/maq, a short read mapping assembler +EAPI=8 +HOMEPAGE=http://maq.sourceforge.net/ +INHERIT=autotools +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_=gnuconfig b6b3e92f8b8c996400074b5f61a59256 toolchain-funcs e9da88162e7a3c60376e80c2c2adcdfb multilib 4fbbbc98f236f1b43acd99476bc3cd85 libtool 241a8f577b9781a42a7421e53448a44e autotools 2fd69a56a527d12409ba43c733b7ac8f +_md5_=ce6e22a8dca500f24263e27d73b9eda4 diff --git a/metadata/md5-cache/sci-biology/mummer-3.23 b/metadata/md5-cache/sci-biology/mummer-3.23 deleted file mode 100644 index 2383fa9b129d..000000000000 --- a/metadata/md5-cache/sci-biology/mummer-3.23 +++ /dev/null @@ -1,13 +0,0 @@ -DEFINED_PHASES=configure install -DESCRIPTION=A rapid whole genome aligner -EAPI=6 -HOMEPAGE=http://mummer.sourceforge.net/ -INHERIT=flag-o-matic toolchain-funcs -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_=toolchain-funcs e9da88162e7a3c60376e80c2c2adcdfb multilib 4fbbbc98f236f1b43acd99476bc3cd85 desktop 22952d8f27cac191d75529d4c38e6bfa edos2unix 33e347e171066657f91f8b0c72ec8773 estack 055c42df72f76a4f45ec92b35e83cd56 epatch 28f0f3c0226306ec5f49e13bf851f171 ltprune 97143780d341cc8d8f1d4c6187a36d29 preserve-libs a8e50acee31b5759b4df1f7707cae54b strip-linguas ac3ee41ee2d31d8c41a77c0838320cc7 vcs-clean d271b7bc7e6a009758d7d4ef749174e3 wrapper 4a1902f969e5718126434fc35f3a0d9c eutils dab5d8ec471d025b79c9e6906bcf3bff flag-o-matic a3abd6002fafb3022597be6b8d01f88b -_md5_=c256f298b416306c1be7005e7877f7b9 diff --git a/metadata/md5-cache/sci-biology/mummer-3.23-r1 b/metadata/md5-cache/sci-biology/mummer-3.23-r1 new file mode 100644 index 000000000000..670efbee9569 --- /dev/null +++ b/metadata/md5-cache/sci-biology/mummer-3.23-r1 @@ -0,0 +1,13 @@ +DEFINED_PHASES=configure install +DESCRIPTION=A rapid whole genome aligner +EAPI=8 +HOMEPAGE=http://mummer.sourceforge.net/ +INHERIT=flag-o-matic toolchain-funcs +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_=toolchain-funcs e9da88162e7a3c60376e80c2c2adcdfb multilib 4fbbbc98f236f1b43acd99476bc3cd85 flag-o-matic a3abd6002fafb3022597be6b8d01f88b +_md5_=7103f6fc8a8d965ba2e5b71b09010e1d diff --git a/metadata/md5-cache/sci-biology/pals-1.0-r1 b/metadata/md5-cache/sci-biology/pals-1.0-r1 deleted file mode 100644 index 09ab2f9536f6..000000000000 --- a/metadata/md5-cache/sci-biology/pals-1.0-r1 +++ /dev/null @@ -1,11 +0,0 @@ -DEFINED_PHASES=configure install -DESCRIPTION=Pairwise Aligner for Long Sequences -EAPI=6 -HOMEPAGE=http://www.drive5.com/pals/ -INHERIT=toolchain-funcs -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_=toolchain-funcs e9da88162e7a3c60376e80c2c2adcdfb multilib 4fbbbc98f236f1b43acd99476bc3cd85 -_md5_=b0df20d47905df6a290c5fe2f79fd48b diff --git a/metadata/md5-cache/sci-biology/pals-1.0-r2 b/metadata/md5-cache/sci-biology/pals-1.0-r2 new file mode 100644 index 000000000000..ead6a9896af6 --- /dev/null +++ b/metadata/md5-cache/sci-biology/pals-1.0-r2 @@ -0,0 +1,11 @@ +DEFINED_PHASES=configure install +DESCRIPTION=Pairwise Aligner for Long Sequences +EAPI=8 +HOMEPAGE=http://www.drive5.com/pals/ +INHERIT=toolchain-funcs +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_=toolchain-funcs e9da88162e7a3c60376e80c2c2adcdfb multilib 4fbbbc98f236f1b43acd99476bc3cd85 +_md5_=0374a4cc1893f560fdb963ab9e27c56b diff --git a/metadata/md5-cache/sci-biology/phred-071220-r1 b/metadata/md5-cache/sci-biology/phred-071220-r1 deleted file mode 100644 index 4f6b8e22eee3..000000000000 --- a/metadata/md5-cache/sci-biology/phred-071220-r1 +++ /dev/null @@ -1,12 +0,0 @@ -DEFINED_PHASES=compile install nofetch -DESCRIPTION=A base caller for Sanger DNA sequencing -EAPI=6 -HOMEPAGE=http://phrap.org/phredphrapconsed.html -INHERIT=toolchain-funcs -KEYWORDS=~amd64 ~x86 -LICENSE=phrap -RESTRICT=fetch -SLOT=0 -SRC_URI=phred-dist-071220.b-acd.tar.gz -_eclasses_=toolchain-funcs e9da88162e7a3c60376e80c2c2adcdfb multilib 4fbbbc98f236f1b43acd99476bc3cd85 -_md5_=6cb07f602eee34da61fd893818f30936 diff --git a/metadata/md5-cache/sci-biology/phred-071220-r2 b/metadata/md5-cache/sci-biology/phred-071220-r2 new file mode 100644 index 000000000000..c59c08039029 --- /dev/null +++ b/metadata/md5-cache/sci-biology/phred-071220-r2 @@ -0,0 +1,12 @@ +DEFINED_PHASES=compile install nofetch +DESCRIPTION=A base caller for Sanger DNA sequencing +EAPI=8 +HOMEPAGE=http://phrap.org/phredphrapconsed.html +INHERIT=toolchain-funcs +KEYWORDS=~amd64 ~x86 +LICENSE=phrap +RESTRICT=fetch +SLOT=0 +SRC_URI=phred-dist-071220.b-acd.tar.gz +_eclasses_=toolchain-funcs e9da88162e7a3c60376e80c2c2adcdfb multilib 4fbbbc98f236f1b43acd99476bc3cd85 +_md5_=b4f0ecabb29f6151604a63619790300c diff --git a/metadata/md5-cache/sci-biology/phyml-2.4.5-r3 b/metadata/md5-cache/sci-biology/phyml-2.4.5-r3 deleted file mode 100644 index 34c540a2e1e2..000000000000 --- a/metadata/md5-cache/sci-biology/phyml-2.4.5-r3 +++ /dev/null @@ -1,11 +0,0 @@ -DEFINED_PHASES=install prepare -DESCRIPTION=Estimation of large phylogenies by maximum likelihood -EAPI=6 -HOMEPAGE=http://atgc.lirmm.fr/phyml/ -INHERIT=toolchain-funcs -KEYWORDS=amd64 ~ppc x86 -LICENSE=GPL-2 -SLOT=0 -SRC_URI=http://www.lirmm.fr/~guindon/phyml_v2.4.5.tar.gz -_eclasses_=toolchain-funcs e9da88162e7a3c60376e80c2c2adcdfb multilib 4fbbbc98f236f1b43acd99476bc3cd85 -_md5_=8909f510fa1072825fa60fbc8a72920e diff --git a/metadata/md5-cache/sci-biology/phyml-2.4.5-r4 b/metadata/md5-cache/sci-biology/phyml-2.4.5-r4 new file mode 100644 index 000000000000..e4800cea2fcc --- /dev/null +++ b/metadata/md5-cache/sci-biology/phyml-2.4.5-r4 @@ -0,0 +1,11 @@ +DEFINED_PHASES=configure install +DESCRIPTION=Estimation of large phylogenies by maximum likelihood +EAPI=8 +HOMEPAGE=http://atgc.lirmm.fr/phyml/ +INHERIT=toolchain-funcs +KEYWORDS=amd64 ~ppc x86 +LICENSE=GPL-2 +SLOT=0 +SRC_URI=http://www.lirmm.fr/~guindon/phyml_v2.4.5.tar.gz +_eclasses_=toolchain-funcs e9da88162e7a3c60376e80c2c2adcdfb multilib 4fbbbc98f236f1b43acd99476bc3cd85 +_md5_=d7f38a7c0005dca5f3da1d1fbd9780ae diff --git a/metadata/md5-cache/sci-biology/piler-1.0-r1 b/metadata/md5-cache/sci-biology/piler-1.0-r1 deleted file mode 100644 index 5641b33a3359..000000000000 --- a/metadata/md5-cache/sci-biology/piler-1.0-r1 +++ /dev/null @@ -1,12 +0,0 @@ -DEFINED_PHASES=configure install -DESCRIPTION=Analysis of repetitive DNA found in genome sequences -EAPI=6 -HOMEPAGE=http://www.drive5.com/piler/ -INHERIT=toolchain-funcs -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_=toolchain-funcs e9da88162e7a3c60376e80c2c2adcdfb multilib 4fbbbc98f236f1b43acd99476bc3cd85 -_md5_=7b5a6d618aac08240cf165a04509c319 diff --git a/metadata/md5-cache/sci-biology/piler-1.0-r2 b/metadata/md5-cache/sci-biology/piler-1.0-r2 new file mode 100644 index 000000000000..7f660db458c7 --- /dev/null +++ b/metadata/md5-cache/sci-biology/piler-1.0-r2 @@ -0,0 +1,12 @@ +DEFINED_PHASES=configure install +DESCRIPTION=Analysis of repetitive DNA found in genome sequences +EAPI=8 +HOMEPAGE=http://www.drive5.com/piler/ +INHERIT=toolchain-funcs +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_=toolchain-funcs e9da88162e7a3c60376e80c2c2adcdfb multilib 4fbbbc98f236f1b43acd99476bc3cd85 +_md5_=5a8dffca1e2b80e93cf1efdff5fd3fd0 diff --git a/metadata/md5-cache/sci-biology/pilercr-1.0-r1 b/metadata/md5-cache/sci-biology/pilercr-1.0-r1 deleted file mode 100644 index c1952ad55f34..000000000000 --- a/metadata/md5-cache/sci-biology/pilercr-1.0-r1 +++ /dev/null @@ -1,11 +0,0 @@ -DEFINED_PHASES=configure install -DESCRIPTION=Analysis of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) -EAPI=6 -HOMEPAGE=http://www.drive5.com/pilercr/ -INHERIT=toolchain-funcs -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_=toolchain-funcs e9da88162e7a3c60376e80c2c2adcdfb multilib 4fbbbc98f236f1b43acd99476bc3cd85 -_md5_=d9f7901d3776c424cfb93782cc6ddafa diff --git a/metadata/md5-cache/sci-biology/pilercr-1.0-r2 b/metadata/md5-cache/sci-biology/pilercr-1.0-r2 new file mode 100644 index 000000000000..140787e0ed04 --- /dev/null +++ b/metadata/md5-cache/sci-biology/pilercr-1.0-r2 @@ -0,0 +1,11 @@ +DEFINED_PHASES=configure install +DESCRIPTION=Analysis of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) +EAPI=8 +HOMEPAGE=http://www.drive5.com/pilercr/ +INHERIT=toolchain-funcs +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_=toolchain-funcs e9da88162e7a3c60376e80c2c2adcdfb multilib 4fbbbc98f236f1b43acd99476bc3cd85 +_md5_=d6fca147863ed9ae98f77d0b6f762060 diff --git a/metadata/md5-cache/sci-biology/prank-140603 b/metadata/md5-cache/sci-biology/prank-140603 deleted file mode 100644 index 3951a97f8de1..000000000000 --- a/metadata/md5-cache/sci-biology/prank-140603 +++ /dev/null @@ -1,11 +0,0 @@ -DEFINED_PHASES=compile install prepare -DESCRIPTION=Probabilistic Alignment Kit -EAPI=6 -HOMEPAGE=http://wasabiapp.org/software/prank/ -INHERIT=toolchain-funcs -KEYWORDS=~amd64 ~x86 -LICENSE=GPL-3 -SLOT=0 -SRC_URI=http://wasabiapp.org/download/prank/prank.source.140603.tgz -_eclasses_=toolchain-funcs e9da88162e7a3c60376e80c2c2adcdfb multilib 4fbbbc98f236f1b43acd99476bc3cd85 -_md5_=17023476000980284365a9c0ed04a6f0 diff --git a/metadata/md5-cache/sci-biology/prank-140603-r1 b/metadata/md5-cache/sci-biology/prank-140603-r1 new file mode 100644 index 000000000000..584c61ad9b18 --- /dev/null +++ b/metadata/md5-cache/sci-biology/prank-140603-r1 @@ -0,0 +1,11 @@ +DEFINED_PHASES=configure install +DESCRIPTION=Probabilistic Alignment Kit +EAPI=8 +HOMEPAGE=http://wasabiapp.org/software/prank/ +INHERIT=toolchain-funcs +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-3 +SLOT=0 +SRC_URI=http://wasabiapp.org/download/prank/prank.source.140603.tgz +_eclasses_=toolchain-funcs e9da88162e7a3c60376e80c2c2adcdfb multilib 4fbbbc98f236f1b43acd99476bc3cd85 +_md5_=07f1836dd1c44c4ebf19bb6a59f7141a diff --git a/metadata/md5-cache/sci-biology/prodigal-2.6.3 b/metadata/md5-cache/sci-biology/prodigal-2.6.3 deleted file mode 100644 index ecbdb3a4bb25..000000000000 --- a/metadata/md5-cache/sci-biology/prodigal-2.6.3 +++ /dev/null @@ -1,11 +0,0 @@ -DEFINED_PHASES=configure -DESCRIPTION=Prokaryotic Dynamic Programming Genefinding Algorithm -EAPI=6 -HOMEPAGE=http://prodigal.ornl.gov/ -INHERIT=toolchain-funcs -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_=toolchain-funcs e9da88162e7a3c60376e80c2c2adcdfb multilib 4fbbbc98f236f1b43acd99476bc3cd85 -_md5_=9cea3bcc55e864076d7e4b542f657f96 diff --git a/metadata/md5-cache/sci-biology/prodigal-2.6.3-r1 b/metadata/md5-cache/sci-biology/prodigal-2.6.3-r1 new file mode 100644 index 000000000000..1b862f2cfb5b --- /dev/null +++ b/metadata/md5-cache/sci-biology/prodigal-2.6.3-r1 @@ -0,0 +1,11 @@ +DEFINED_PHASES=configure +DESCRIPTION=Prokaryotic Dynamic Programming Genefinding Algorithm +EAPI=8 +HOMEPAGE=http://prodigal.ornl.gov/ +INHERIT=toolchain-funcs +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_=toolchain-funcs e9da88162e7a3c60376e80c2c2adcdfb multilib 4fbbbc98f236f1b43acd99476bc3cd85 +_md5_=fbd84f84d9eeda38c197893cf2c079c8 diff --git a/metadata/md5-cache/sci-biology/recon-1.08 b/metadata/md5-cache/sci-biology/recon-1.08 deleted file mode 100644 index 9e9e4eb623bb..000000000000 --- a/metadata/md5-cache/sci-biology/recon-1.08 +++ /dev/null @@ -1,13 +0,0 @@ -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 -INHERIT=toolchain-funcs -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_=toolchain-funcs e9da88162e7a3c60376e80c2c2adcdfb multilib 4fbbbc98f236f1b43acd99476bc3cd85 -_md5_=2ddd537d912c7c88b6f0b0d203a51613 diff --git a/metadata/md5-cache/sci-biology/recon-1.08-r1 b/metadata/md5-cache/sci-biology/recon-1.08-r1 new file mode 100644 index 000000000000..6171695c1e65 --- /dev/null +++ b/metadata/md5-cache/sci-biology/recon-1.08-r1 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile install prepare +DESCRIPTION=Automated de novo identification of repeat families from genomic sequences +EAPI=8 +HOMEPAGE=http://www.repeatmasker.org/RepeatModeler.html +INHERIT=toolchain-funcs +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_=toolchain-funcs e9da88162e7a3c60376e80c2c2adcdfb multilib 4fbbbc98f236f1b43acd99476bc3cd85 +_md5_=36772ec3438da03e296e39fc88b347ee diff --git a/metadata/md5-cache/sci-biology/rnaview-20040713-r4 b/metadata/md5-cache/sci-biology/rnaview-20040713-r4 deleted file mode 100644 index ef7ce4100a57..000000000000 --- a/metadata/md5-cache/sci-biology/rnaview-20040713-r4 +++ /dev/null @@ -1,11 +0,0 @@ -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 -INHERIT=toolchain-funcs -KEYWORDS=~amd64 ~x86 -LICENSE=public-domain -SLOT=0 -SRC_URI=mirror://gentoo/rnaview-20040713.tar.bz2 -_eclasses_=toolchain-funcs e9da88162e7a3c60376e80c2c2adcdfb multilib 4fbbbc98f236f1b43acd99476bc3cd85 -_md5_=788c156d45287bef4f6aa876055bde4c diff --git a/metadata/md5-cache/sci-biology/rnaview-20040713-r5 b/metadata/md5-cache/sci-biology/rnaview-20040713-r5 new file mode 100644 index 000000000000..6d64e471a767 --- /dev/null +++ b/metadata/md5-cache/sci-biology/rnaview-20040713-r5 @@ -0,0 +1,11 @@ +DEFINED_PHASES=configure install +DESCRIPTION=Generates 2D displays of RNA/DNA secondary structures with tertiary interactions +EAPI=8 +HOMEPAGE=http://ndbserver.rutgers.edu/services/download/index.html +INHERIT=toolchain-funcs +KEYWORDS=~amd64 ~x86 +LICENSE=public-domain +SLOT=0 +SRC_URI=mirror://gentoo/rnaview-20040713.tar.bz2 +_eclasses_=toolchain-funcs e9da88162e7a3c60376e80c2c2adcdfb multilib 4fbbbc98f236f1b43acd99476bc3cd85 +_md5_=dd5336243d83138448c13acb7f4d4ba2 diff --git a/metadata/md5-cache/sci-biology/t-coffee-11.00-r2 b/metadata/md5-cache/sci-biology/t-coffee-11.00-r2 deleted file mode 100644 index 6cec0e77ed2b..000000000000 --- a/metadata/md5-cache/sci-biology/t-coffee-11.00-r2 +++ /dev/null @@ -1,12 +0,0 @@ -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 -INHERIT=toolchain-funcs -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_=toolchain-funcs e9da88162e7a3c60376e80c2c2adcdfb multilib 4fbbbc98f236f1b43acd99476bc3cd85 -_md5_=5c54b109c5b8bef93adbc5f99ddd7114 diff --git a/metadata/md5-cache/sci-biology/t-coffee-11.00-r3 b/metadata/md5-cache/sci-biology/t-coffee-11.00-r3 new file mode 100644 index 000000000000..c71a62e9c29c --- /dev/null +++ b/metadata/md5-cache/sci-biology/t-coffee-11.00-r3 @@ -0,0 +1,12 @@ +DEFINED_PHASES=compile configure install +DESCRIPTION=A multiple sequence alignment package +EAPI=8 +HOMEPAGE=http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html +INHERIT=flag-o-matic toolchain-funcs +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_=toolchain-funcs e9da88162e7a3c60376e80c2c2adcdfb multilib 4fbbbc98f236f1b43acd99476bc3cd85 flag-o-matic a3abd6002fafb3022597be6b8d01f88b +_md5_=4f19327a55b73328939540ced2179d21 diff --git a/metadata/md5-cache/sci-biology/transfac-3.2-r1 b/metadata/md5-cache/sci-biology/transfac-3.2-r1 deleted file mode 100644 index 91dec5eae8be..000000000000 --- a/metadata/md5-cache/sci-biology/transfac-3.2-r1 +++ /dev/null @@ -1,12 +0,0 @@ -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/transfac-3.2-r2 b/metadata/md5-cache/sci-biology/transfac-3.2-r2 new file mode 100644 index 000000000000..4c28d14c7975 --- /dev/null +++ b/metadata/md5-cache/sci-biology/transfac-3.2-r2 @@ -0,0 +1,12 @@ +BDEPEND=emboss? ( sci-biology/emboss ) +DEFINED_PHASES=compile install +DESCRIPTION=A database of eucaryotic transcription factors +EAPI=8 +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_=6312c1bc4fc292848eed00fb67efa7c9 diff --git a/metadata/md5-cache/sci-biology/trf-4.04-r1 b/metadata/md5-cache/sci-biology/trf-4.04-r1 deleted file mode 100644 index 3195b5c5feec..000000000000 --- a/metadata/md5-cache/sci-biology/trf-4.04-r1 +++ /dev/null @@ -1,10 +0,0 @@ -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/trf-4.04-r2 b/metadata/md5-cache/sci-biology/trf-4.04-r2 new file mode 100644 index 000000000000..30e1962524fe --- /dev/null +++ b/metadata/md5-cache/sci-biology/trf-4.04-r2 @@ -0,0 +1,10 @@ +DEFINED_PHASES=install unpack +DESCRIPTION=Tandem Repeats Finder +EAPI=8 +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_=7a6d356b931b70a39c33d922bd23adb1 diff --git a/metadata/md5-cache/sci-biology/yass-1.14-r2 b/metadata/md5-cache/sci-biology/yass-1.14-r2 deleted file mode 100644 index cafc0a5daadc..000000000000 --- a/metadata/md5-cache/sci-biology/yass-1.14-r2 +++ /dev/null @@ -1,14 +0,0 @@ -DEFINED_PHASES=configure prepare -DEPEND=dmalloc? ( dev-libs/dmalloc ) sys-devel/gnuconfig >=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.5:1.16 ) >=sys-devel/autoconf-2.71 >=sys-devel/libtool-2.4 -DESCRIPTION=Genomic similarity search with multiple transition constrained spaced seeds -EAPI=6 -HOMEPAGE=http://bioinfo.lifl.fr/yass/ -INHERIT=autotools -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_=desktop 22952d8f27cac191d75529d4c38e6bfa edos2unix 33e347e171066657f91f8b0c72ec8773 estack 055c42df72f76a4f45ec92b35e83cd56 epatch 28f0f3c0226306ec5f49e13bf851f171 toolchain-funcs e9da88162e7a3c60376e80c2c2adcdfb multilib 4fbbbc98f236f1b43acd99476bc3cd85 ltprune 97143780d341cc8d8f1d4c6187a36d29 preserve-libs a8e50acee31b5759b4df1f7707cae54b strip-linguas ac3ee41ee2d31d8c41a77c0838320cc7 vcs-clean d271b7bc7e6a009758d7d4ef749174e3 wrapper 4a1902f969e5718126434fc35f3a0d9c eutils dab5d8ec471d025b79c9e6906bcf3bff gnuconfig b6b3e92f8b8c996400074b5f61a59256 libtool 241a8f577b9781a42a7421e53448a44e autotools 2fd69a56a527d12409ba43c733b7ac8f -_md5_=3a4ba9b4e7b8efec51cfc79d261fefd3 diff --git a/metadata/md5-cache/sci-biology/yass-1.14-r3 b/metadata/md5-cache/sci-biology/yass-1.14-r3 new file mode 100644 index 000000000000..5d07f61e5a18 --- /dev/null +++ b/metadata/md5-cache/sci-biology/yass-1.14-r3 @@ -0,0 +1,15 @@ +BDEPEND=sys-devel/gnuconfig >=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.5:1.16 ) >=sys-devel/autoconf-2.71 >=sys-devel/libtool-2.4 +DEFINED_PHASES=configure prepare +DEPEND=dmalloc? ( dev-libs/dmalloc ) +DESCRIPTION=Genomic similarity search with multiple transition constrained spaced seeds +EAPI=8 +HOMEPAGE=http://bioinfo.lifl.fr/yass/ +INHERIT=autotools +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_=gnuconfig b6b3e92f8b8c996400074b5f61a59256 toolchain-funcs e9da88162e7a3c60376e80c2c2adcdfb multilib 4fbbbc98f236f1b43acd99476bc3cd85 libtool 241a8f577b9781a42a7421e53448a44e autotools 2fd69a56a527d12409ba43c733b7ac8f +_md5_=9e0eb1b35801ce703a9a397be6421d47 diff --git a/metadata/pkg_desc_index b/metadata/pkg_desc_index index f3005603cccf..7c145a6e9c2f 100644 --- a/metadata/pkg_desc_index +++ b/metadata/pkg_desc_index @@ -16375,34 +16375,34 @@ sci-biology/HTSeq 2.0.2 9999: Python support for SAM/BAM/Bowtie/FASTA/Q/GFF/GTF sci-biology/STAR 2.7.10a: STAR aligner: align RNA-seq reads to reference genome uncompressed suffix arrays sci-biology/aaindex 9.1-r2: Amino acid indices and similarity matrices sci-biology/abyss 2.3.4: Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler -sci-biology/amap 2.2-r4: Protein multiple-alignment-based sequence annealing +sci-biology/amap 2.2-r5: Protein multiple-alignment-based sequence annealing sci-biology/augustus 2.5.5 3.4.0-r1: Eukaryotic gene predictor sci-biology/bamtools 2.5.2 9999: A programmer's API and an end-user's toolkit for handling BAM files sci-biology/bcftools 1.15.1: Utilities for variant calling and manipulating VCF and BCF files sci-biology/bedtools 2.30.0: Tools for manipulation and analysis of BED, GFF/GTF, VCF, SAM/BAM file formats sci-biology/bfast 0.7.0a: Blat-like Fast Accurate Search Tool -sci-biology/biogrep 1.0-r2: Multithreaded tool for matching large sets of patterns against biosequence DBs +sci-biology/biogrep 1.0-r3: Multithreaded tool for matching large sets of patterns against biosequence DBs sci-biology/biopandas 0.2.7: Molecular Structures in Pandas DataFrames sci-biology/bioperl 1.6.9-r1: Perl tools for bioinformatics - Core modules sci-biology/bioperl-db 1.6.9-r2: Perl tools for bioinformatics - Perl API that accesses the BioSQL schema sci-biology/bioperl-network 1.6.9-r1: Perl tools for bioinformatics - Analysis of protein-protein interaction networks sci-biology/bioperl-run 1.6.9-r1: Perl wrapper modules for key bioinformatics applications sci-biology/biopython 1.79: Python modules for computational molecular biology -sci-biology/biosql 1.0.1-r1: A generic bioinformatics relational database model -sci-biology/blat 34-r2: The BLAST-Like Alignment Tool, a fast genomic sequence aligner +sci-biology/biosql 1.0.1-r2: A generic bioinformatics relational database model +sci-biology/blat 34-r3: The BLAST-Like Alignment Tool, a fast genomic sequence aligner sci-biology/bowtie 2.4.4: Popular short read aligner for Next-generation sequencing data sci-biology/bwa 0.7.17: Burrows-Wheeler Alignment Tool, a fast short genomic sequence aligner -sci-biology/cd-hit 4.6.6: Clustering Database at High Identity with Tolerance -sci-biology/clustal-omega 1.2.4: Scalable multiple alignment of protein sequences -sci-biology/clustalw 1.83-r4 2.1-r1: General purpose multiple alignment program for DNA and proteins +sci-biology/cd-hit 4.6.6-r1: Clustering Database at High Identity with Tolerance +sci-biology/clustal-omega 1.2.4-r1: Scalable multiple alignment of protein sequences +sci-biology/clustalw 1.83-r4 2.1-r2: General purpose multiple alignment program for DNA and proteins sci-biology/clustalw-mpi 0.13-r3: An MPI implemention of the ClustalW general purpose multiple alignment algorithm sci-biology/clustalx 2.1-r3: Graphical interface for the ClustalW multiple alignment program sci-biology/consed 29: A genome sequence finishing program sci-biology/cutg 160-r1: Codon usage tables calculated from GenBank sci-biology/dialign-tx 1.0.2-r2: Greedy and progressive approaches for segment-based multiple sequence alignment -sci-biology/dialign2 2.2.1: Multiple sequence alignment -sci-biology/elph 1.0.1-r1: Estimated Locations of Pattern Hits - Motif finder program -sci-biology/embassy 6.6.0-r2: A meta-package for installing all EMBASSY packages (EMBOSS add-ons) +sci-biology/dialign2 2.2.1-r1: Multiple sequence alignment +sci-biology/elph 1.0.1-r2: Estimated Locations of Pattern Hits - Motif finder program +sci-biology/embassy 6.6.0-r3: A meta-package for installing all EMBASSY packages (EMBOSS add-ons) sci-biology/embassy-cbstools 1.0.0.660-r1: EMBOSS integrated version of Applications from the CBS group sci-biology/embassy-clustalomega 1.1.0.660-r1: EMBOSS integrated version of Clustal Omega - Multiple Sequence Alignment sci-biology/embassy-domainatrix 0.1.660-r1: EMBOSS integrated version of Protein domain analysis add-on package @@ -16419,8 +16419,8 @@ sci-biology/embassy-structure 0.1.660-r1: EMBOSS integrated version of Protein s sci-biology/embassy-topo 2.0.660-r1: EMBOSS integrated version of Transmembrane protein display sci-biology/embassy-vienna 1.7.2.660-r1: EMBOSS integrated version of Vienna RNA package - RNA folding sci-biology/emboss 6.6.0-r2: The European Molecular Biology Open Software Suite - A sequence analysis package -sci-biology/eugene 4.1d: Prokaryotic and Eukaryotic gene predictor -sci-biology/exonerate 2.2.0-r2: Generic tool for pairwise sequence comparison +sci-biology/eugene 4.1d-r1: Prokaryotic and Eukaryotic gene predictor +sci-biology/exonerate 2.2.0-r3: Generic tool for pairwise sequence comparison sci-biology/express 1.5.1: Streaming RNA-Seq Analysis sci-biology/fasta 36.3.8h-r1: FASTA is a DNA and Protein sequence alignment software package sci-biology/fasttree 2.1.11: Fast inference of approximately-maximum-likelihood phylogenetic trees @@ -16430,58 +16430,58 @@ sci-biology/foldingathome 7.6.13-r1 7.6.21: Folding@Home is a distributed comput sci-biology/glimmer 3.02b: An HMM-based microbial gene finding system from TIGR sci-biology/glimmerhmm 3.0.1-r1: A eukaryotic gene finding system from TIGR sci-biology/gmap 2020.10.27: A Genomic Mapping and Alignment Program for mRNA and EST Sequences -sci-biology/hmmer 2.3.2-r4 3.1_beta2: Sequence analysis using profile hidden Markov models -sci-biology/iedera 1.05-r1: A subset seed design tool for DNA sequence alignment +sci-biology/hmmer 2.3.2-r5 3.1_beta2-r1: Sequence analysis using profile hidden Markov models +sci-biology/iedera 1.05-r2: A subset seed design tool for DNA sequence alignment sci-biology/infernal 1.0.2-r1: Inference of RNA alignments -sci-biology/iqpnni 3.3.2-r1: Important Quartet Puzzling and NNI Operation -sci-biology/kalign 2.03-r2: Global and progressive multiple sequence alignment +sci-biology/iqpnni 3.3.2-r2: Important Quartet Puzzling and NNI Operation +sci-biology/kalign 2.03-r3: Global and progressive multiple sequence alignment sci-biology/kallisto 0.46.2: Near-optimal RNA-Seq quantification sci-biology/lagan 2.0-r4: The LAGAN suite of tools for whole-genome multiple alignment of genomic DNA sci-biology/libgtextutils 0.6.1-r1: Gordon Text utils Library sci-biology/mafft 7.490: Multiple sequence alignments using a variety of algorithms -sci-biology/maq 0.7.1-r2: Mapping and Assembly with Qualities, mapping NGS reads to reference genomes -sci-biology/maqview 0.2.5-r3: GUI for sci-biology/maq, a short read mapping assembler +sci-biology/maq 0.7.1-r3: Mapping and Assembly with Qualities, mapping NGS reads to reference genomes +sci-biology/maqview 0.2.5-r4: GUI for sci-biology/maq, a short read mapping assembler sci-biology/mcl 14.137: A Markov Cluster Algorithm implementation sci-biology/mosaik 2.2.30: A reference-guided aligner for next-generation sequencing technologies sci-biology/mothur 1.27.0-r1: A suite of algorithms for ecological bioinformatics sci-biology/mrbayes 3.1.2-r2 3.2.7: Bayesian Inference of Phylogeny -sci-biology/mummer 3.23: A rapid whole genome aligner +sci-biology/mummer 3.23-r1: A rapid whole genome aligner sci-biology/muscle 3.8.31: Multiple sequence comparison by log-expectation sci-biology/newick-utils 1.6-r1: Tools for processing phylogenetic trees -sci-biology/pals 1.0-r1: Pairwise Aligner for Long Sequences +sci-biology/pals 1.0-r2: Pairwise Aligner for Long Sequences sci-biology/paml 4.9j: Phylogenetic Analysis by Maximum Likelihood sci-biology/phrap 1.080812-r2: Shotgun assembly and alignment utilities -sci-biology/phred 071220-r1: A base caller for Sanger DNA sequencing +sci-biology/phred 071220-r2: A base caller for Sanger DNA sequencing sci-biology/phylip 3.698: The PHYLogeny Inference Package -sci-biology/phyml 2.4.5-r3: Estimation of large phylogenies by maximum likelihood -sci-biology/piler 1.0-r1: Analysis of repetitive DNA found in genome sequences -sci-biology/pilercr 1.0-r1: Analysis of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) +sci-biology/phyml 2.4.5-r4: Estimation of large phylogenies by maximum likelihood +sci-biology/piler 1.0-r2: Analysis of repetitive DNA found in genome sequences +sci-biology/pilercr 1.0-r2: Analysis of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) sci-biology/plink 1.90_pre140514: Whole genome association analysis toolset sci-biology/poa 2-r1: Fast multiple sequence alignments using partial-order graphs -sci-biology/prank 140603: Probabilistic Alignment Kit +sci-biology/prank 140603-r1: Probabilistic Alignment Kit sci-biology/primer3 2.3.7-r1: Primer Design for PCR reactions sci-biology/prints 39.0-r2: A protein motif fingerprint database sci-biology/probcons 1.12-r1: Probabilistic Consistency-based Multiple Alignment of Amino Acid Sequences -sci-biology/prodigal 2.6.3: Prokaryotic Dynamic Programming Genefinding Algorithm +sci-biology/prodigal 2.6.3-r1: Prokaryotic Dynamic Programming Genefinding Algorithm sci-biology/profphd 1.0.40: Secondary structure and solvent accessibility predictor sci-biology/prosite 2017.02-r1: A protein families and domains database sci-biology/pysam 0.19.1: Python interface for the SAM/BAM sequence alignment and mapping format sci-biology/qrna 2.0.3c-r3: Prototype ncRNA genefinder sci-biology/raxml 7.2.6: Sequential, Parallel & Distributed Inference of Large Phylogenetic Trees sci-biology/rebase 1901-r1: A restriction enzyme database -sci-biology/recon 1.08: Automated de novo identification of repeat families from genomic sequences -sci-biology/rnaview 20040713-r4: Generates 2D displays of RNA/DNA secondary structures with tertiary interactions +sci-biology/recon 1.08-r1: Automated de novo identification of repeat families from genomic sequences +sci-biology/rnaview 20040713-r5: Generates 2D displays of RNA/DNA secondary structures with tertiary interactions sci-biology/samtools 0.1.20-r4 1.15.1: Utilities for analysing and manipulating the SAM/BAM alignment formats sci-biology/seaview 4.6-r1: A graphical multiple sequence alignment editor sci-biology/seqan 2.4.0-r1 3.1.0: C++ Sequence Analysis Library sci-biology/sibsim4 0.20: A rewrite and improvement upon sim4, a DNA-mRNA aligner sci-biology/sim4 20030921-r2: A program to align cDNA and genomic DNA sci-biology/stride 20011129-r1: Protein secondary structure assignment from atomic coordinates -sci-biology/t-coffee 11.00-r2: A multiple sequence alignment package -sci-biology/transfac 3.2-r1: A database of eucaryotic transcription factors +sci-biology/t-coffee 11.00-r3: A multiple sequence alignment package +sci-biology/transfac 3.2-r2: A database of eucaryotic transcription factors sci-biology/tree-puzzle 5.2: Maximum likelihood analysis for nucleotide, amino acid, and two-state data sci-biology/treeviewx 0.5.1-r3: A phylogenetic tree viewer -sci-biology/trf 4.04-r1: Tandem Repeats Finder +sci-biology/trf 4.04-r2: Tandem Repeats Finder sci-biology/trnascan-se 1.31 1.31-r1: tRNA detection in large-scale genome sequences sci-biology/uchime 4.2.40: Fast, accurate chimera detection sci-biology/ucsc-genome-browser 260-r1: The UCSC genome browser suite, also known as Jim Kent's library and GoldenPath @@ -16490,7 +16490,7 @@ sci-biology/update-blastdb 12.0.0: update_blastdb.pl for local blast db maintain sci-biology/vcftools 0.1.16: Tools for working with VCF (Variant Call Format) files sci-biology/velvet 1.2.10: A sequence assembler for very short reads sci-biology/wise 2.4.0_alpha-r1: Intelligent algorithms for DNA searches -sci-biology/yass 1.14-r2: Genomic similarity search with multiple transition constrained spaced seeds +sci-biology/yass 1.14-r3: Genomic similarity search with multiple transition constrained spaced seeds sci-calculators/bc-gh 5.2.1 5.3.3: Implementation of POSIX bc with GNU extensions sci-calculators/calcoo 1.3.18-r1: Scientific calculator designed to provide maximum usability sci-calculators/datamash 1.7-r1: command-line program for basic numeric, textual and statistical operations diff --git a/metadata/timestamp.chk b/metadata/timestamp.chk index b781160d353c..0c936d6bc781 100644 --- a/metadata/timestamp.chk +++ b/metadata/timestamp.chk @@ -1 +1 @@ -Thu, 07 Jul 2022 19:46:30 +0000 +Thu, 07 Jul 2022 20:01:43 +0000 diff --git a/profiles/use.local.desc b/profiles/use.local.desc index 1da75958a13c..cb512adcd797 100644 --- a/profiles/use.local.desc +++ b/profiles/use.local.desc @@ -7103,7 +7103,7 @@ sci-biology/bioperl:network - Install sci-biology/bioperl-run sci-biology/bioperl:run - Install sci-biology/bioperl-run sci-biology/clustalw-mpi:mpi-njtree - Use MPI (as opposed to serial) code for computing neighbor-joining trees sci-biology/clustalw-mpi:static-pairalign - Use static (as opposed to dynamic) scheduling for pair alignments -sci-biology/exonerate:utils - Install all utilities +sci-biology/exonerate:utils - Install the follow binaries: esd2esi, fasta2esd, fastaannotatecdna, fastachecksum, fastaclean, fastaclip, fastacomposition, fastadiff, fastaexplode, fastafetch, fastahardmask, fastaindex, fastalength, fastanrdb, fastaoverlap, fastareformat, fastaremove, fastarevcomp, fastasoftmask, fastasort, fastasplit, fastasubseq, fastatranslate, fastavalidcds sci-biology/fasttree:double-precision - use double precision instead of single-precision floating point (2x memroy required) sci-biology/mcl:blast - Add support for NCBI BLAST data sci-biology/newick-utils:xml - Uses dev-libs/libxml2 to handle ornaments -- cgit v1.2.3-65-gdbad