2022-07-07 20:01:43 UTC

53 files changed, 288 insertions, 279 deletions

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-r2
index 2a7fa17d9aa9..54c0036aa974 100644
--- a/metadata/md5-cache/sci-biology/biosql-1.0.1-r1
+++ b/metadata/md5-cache/sci-biology/biosql-1.0.1-r2
@@ -1,7 +1,7 @@
 DEFINED_PHASES=install postinst
 DEPEND=mysql? ( dev-perl/DBD-mysql ) postgres? ( dev-perl/DBD-Pg )
 DESCRIPTION=A generic bioinformatics relational database model
-EAPI=6
+EAPI=8
 HOMEPAGE=http://www.biosql.org/
 IUSE=mysql postgres
 KEYWORDS=amd64 x86
@@ -9,4 +9,4 @@ 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
+_md5_=6438fefd6b37886a8a237f7e9b0c1258
diff --git a/metadata/md5-cache/sci-biology/blat-34-r2 b/metadata/md5-cache/sci-biology/blat-34-r3
index b4f51041763c..9a84ea37c00a 100644
--- a/metadata/md5-cache/sci-biology/blat-34-r2
+++ b/metadata/md5-cache/sci-biology/blat-34-r3
@@ -1,7 +1,7 @@
+BDEPEND=app-arch/unzip
 DEFINED_PHASES=compile install
-DEPEND=app-arch/unzip
 DESCRIPTION=The BLAST-Like Alignment Tool, a fast genomic sequence aligner
-EAPI=6
+EAPI=8
 HOMEPAGE=http://www.cse.ucsc.edu/~kent/
 INHERIT=toolchain-funcs
 KEYWORDS=~amd64 ~x86
@@ -9,4 +9,4 @@ LICENSE=blat
 SLOT=0
 SRC_URI=http://www.soe.ucsc.edu/~kent/src/blatSrc34.zip
 _eclasses_=toolchain-funcs	e9da88162e7a3c60376e80c2c2adcdfb	multilib	4fbbbc98f236f1b43acd99476bc3cd85
-_md5_=9fb0b819fe1d2fa16c86c748d885fc84
+_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-r2
index 4efa2f629660..7b122c7fd0d2 100644
--- a/metadata/md5-cache/sci-biology/clustalw-2.1-r1
+++ b/metadata/md5-cache/sci-biology/clustalw-2.1-r2
@@ -1,9 +1,9 @@
 DEFINED_PHASES=install
 DESCRIPTION=General purpose multiple alignment program for DNA and proteins
-EAPI=6
+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_=c164ea7c4a56d9c6619a6d13320cb5bd
+_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-r2
index 35839f43cfe4..2242e048acd4 100644
--- a/metadata/md5-cache/sci-biology/elph-1.0.1-r1
+++ b/metadata/md5-cache/sci-biology/elph-1.0.1-r2
@@ -1,6 +1,6 @@
 DEFINED_PHASES=configure install
 DESCRIPTION=Estimated Locations of Pattern Hits - Motif finder program
-EAPI=6
+EAPI=8
 HOMEPAGE=http://cbcb.umd.edu/software/ELPH/
 INHERIT=toolchain-funcs
 KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos
@@ -8,4 +8,4 @@ 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
+_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-r3
index da79487711b8..0e21d758fe16 100644
--- a/metadata/md5-cache/sci-biology/embassy-6.6.0-r2
+++ b/metadata/md5-cache/sci-biology/embassy-6.6.0-r3
@@ -1,9 +1,9 @@
 DEFINED_PHASES=-
 DESCRIPTION=A meta-package for installing all EMBASSY packages (EMBOSS add-ons)
-EAPI=6
+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_=f0bb78193b5ac077edf12dbcf43e4eb2
+_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
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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:=
+DESCRIPTION=Prokaryotic and Eukaryotic gene predictor
+EAPI=8
+HOMEPAGE=http://eugene.toulouse.inra.fr/
+INHERIT=autotools
+KEYWORDS=amd64 x86
+LICENSE=Artistic
+RDEPEND=media-libs/gd[png] media-libs/libpng:=
+RESTRICT=test
+SLOT=0
+SRC_URI=https://mulcyber.toulouse.inra.fr/frs/download.php/1359/eugene-4.1d.tar.gz
+_eclasses_=gnuconfig	b6b3e92f8b8c996400074b5f61a59256	toolchain-funcs	e9da88162e7a3c60376e80c2c2adcdfb	multilib	4fbbbc98f236f1b43acd99476bc3cd85	libtool	241a8f577b9781a42a7421e53448a44e	autotools	2fd69a56a527d12409ba43c733b7ac8f
+_md5_=b4126568295c4b4191d28a10bcea4c55
diff --git a/metadata/md5-cache/sci-biology/exonerate-2.2.0-r2 b/metadata/md5-cache/sci-biology/exonerate-2.2.0-r2
deleted file mode 100644
index 61de44722dbf..000000000000
--- a/metadata/md5-cache/sci-biology/exonerate-2.2.0-r2
+++ /dev/null
@@ -1,16 +0,0 @@
-DEFINED_PHASES=configure install prepare
-DEPEND=dev-libs/glib:2 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=Generic tool for pairwise sequence comparison
-EAPI=6
-HOMEPAGE=https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate
-INHERIT=autotools toolchain-funcs
-IUSE=test threads utils
-KEYWORDS=~amd64 ~x86 ~ppc-macos ~x64-macos
-LICENSE=GPL-3
-RDEPEND=dev-libs/glib:2
-REQUIRED_USE=test? ( utils )
-RESTRICT=!test? ( test )
-SLOT=0
-SRC_URI=http://ftp.ebi.ac.uk/pub/software/vertebrategenomics/exonerate/exonerate-2.2.0.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
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diff --git a/metadata/md5-cache/sci-biology/exonerate-2.2.0-r3 b/metadata/md5-cache/sci-biology/exonerate-2.2.0-r3
new file mode 100644
index 000000000000..c9790b5b60cf
--- /dev/null
+++ b/metadata/md5-cache/sci-biology/exonerate-2.2.0-r3
@@ -0,0 +1,17 @@
+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 install prepare
+DEPEND=dev-libs/glib:2
+DESCRIPTION=Generic tool for pairwise sequence comparison
+EAPI=8
+HOMEPAGE=https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate
+INHERIT=autotools toolchain-funcs
+IUSE=test utils
+KEYWORDS=~amd64 ~x86 ~ppc-macos ~x64-macos
+LICENSE=GPL-3
+RDEPEND=dev-libs/glib:2
+REQUIRED_USE=test? ( utils )
+RESTRICT=!test? ( test )
+SLOT=0
+SRC_URI=http://ftp.ebi.ac.uk/pub/software/vertebrategenomics/exonerate/exonerate-2.2.0.tar.gz
+_eclasses_=gnuconfig	b6b3e92f8b8c996400074b5f61a59256	toolchain-funcs	e9da88162e7a3c60376e80c2c2adcdfb	multilib	4fbbbc98f236f1b43acd99476bc3cd85	libtool	241a8f577b9781a42a7421e53448a44e	autotools	2fd69a56a527d12409ba43c733b7ac8f
+_md5_=1e7139985e79a73dd3eda616d23bafc0
diff --git a/metadata/md5-cache/sci-biology/hmmer-2.3.2-r4 b/metadata/md5-cache/sci-biology/hmmer-2.3.2-r4
deleted file mode 100644
index 9bc345ffd85e..000000000000
--- a/metadata/md5-cache/sci-biology/hmmer-2.3.2-r4
+++ /dev/null
@@ -1,12 +0,0 @@
-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-2.3.2-r5 b/metadata/md5-cache/sci-biology/hmmer-2.3.2-r5
new file mode 100644
index 000000000000..af18440f6be1
--- /dev/null
+++ b/metadata/md5-cache/sci-biology/hmmer-2.3.2-r5
@@ -0,0 +1,14 @@
+BDEPEND=test? ( dev-lang/perl )
+DEFINED_PHASES=compile configure install postinst
+DESCRIPTION=Sequence analysis using profile hidden Markov models
+EAPI=8
+HOMEPAGE=http://hmmer.org/
+INHERIT=toolchain-funcs
+IUSE=cpu_flags_ppc_altivec test
+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
+_eclasses_=toolchain-funcs	e9da88162e7a3c60376e80c2c2adcdfb	multilib	4fbbbc98f236f1b43acd99476bc3cd85
+_md5_=5aebac9d4eaee8ecbd0bff74b7b68c5e
diff --git a/metadata/md5-cache/sci-biology/hmmer-3.1_beta2 b/metadata/md5-cache/sci-biology/hmmer-3.1_beta2
deleted file mode 100644
index 0dfc8524d7bb..000000000000
--- a/metadata/md5-cache/sci-biology/hmmer-3.1_beta2
+++ /dev/null
@@ -1,13 +0,0 @@
-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/hmmer-3.1_beta2-r1 b/metadata/md5-cache/sci-biology/hmmer-3.1_beta2-r1
new file mode 100644
index 000000000000..dbd7cde5f5c6
--- /dev/null
+++ b/metadata/md5-cache/sci-biology/hmmer-3.1_beta2-r1
@@ -0,0 +1,16 @@
+BDEPEND=test? ( dev-lang/perl )
+DEFINED_PHASES=compile configure install
+DEPEND=mpi? ( virtual/mpi ) gsl? ( sci-libs/gsl:= )
+DESCRIPTION=Sequence analysis using profile hidden Markov models
+EAPI=8
+HOMEPAGE=http://hmmer.org/
+INHERIT=toolchain-funcs
+IUSE=cpu_flags_ppc_altivec cpu_flags_x86_sse gsl mpi test
+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
+_eclasses_=toolchain-funcs	e9da88162e7a3c60376e80c2c2adcdfb	multilib	4fbbbc98f236f1b43acd99476bc3cd85
+_md5_=66609c69302596b8671531f5be5cf6c1
diff --git a/metadata/md5-cache/sci-biology/iedera-1.05-r1 b/metadata/md5-cache/sci-biology/iedera-1.05-r1
deleted file mode 100644
index c9255db9b178..000000000000
--- a/metadata/md5-cache/sci-biology/iedera-1.05-r1
+++ /dev/null
@@ -1,12 +0,0 @@
-DEFINED_PHASES=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=A subset seed design tool for DNA sequence alignment
-EAPI=6
-HOMEPAGE=http://bioinfo.lifl.fr/yass/iedera.php
-INHERIT=autotools
-KEYWORDS=~amd64 ~x86
-LICENSE=GPL-2
-SLOT=0
-SRC_URI=http://bioinfo.lifl.fr/yass/files/iedera-1.05.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_=ce77e1e27bd52fed2fd2af52744d6288
diff --git a/metadata/md5-cache/sci-biology/iedera-1.05-r2 b/metadata/md5-cache/sci-biology/iedera-1.05-r2
new file mode 100644
index 000000000000..ac25f47154a9
--- /dev/null
+++ b/metadata/md5-cache/sci-biology/iedera-1.05-r2
@@ -0,0 +1,12 @@
+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
+DESCRIPTION=A subset seed design tool for DNA sequence alignment
+EAPI=8
+HOMEPAGE=http://bioinfo.lifl.fr/yass/iedera.php
+INHERIT=autotools
+KEYWORDS=~amd64 ~x86
+LICENSE=GPL-2
+SLOT=0
+SRC_URI=http://bioinfo.lifl.fr/yass/files/iedera-1.05.tar.gz
+_eclasses_=gnuconfig	b6b3e92f8b8c996400074b5f61a59256	toolchain-funcs	e9da88162e7a3c60376e80c2c2adcdfb	multilib	4fbbbc98f236f1b43acd99476bc3cd85	libtool	241a8f577b9781a42a7421e53448a44e	autotools	2fd69a56a527d12409ba43c733b7ac8f
+_md5_=a94a95bf7657c616d7b48d8bc45068c7
diff --git a/metadata/md5-cache/sci-biology/iqpnni-3.3.2-r1 b/metadata/md5-cache/sci-biology/iqpnni-3.3.2-r2
index 975248a39250..c7959fab6eed 100644
--- a/metadata/md5-cache/sci-biology/iqpnni-3.3.2-r1
+++ b/metadata/md5-cache/sci-biology/iqpnni-3.3.2-r2
@@ -1,10 +1,10 @@
 DEFINED_PHASES=install
 DESCRIPTION=Important Quartet Puzzling and NNI Operation
-EAPI=6
+EAPI=8
 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
+_md5_=6aae6556c487f2f133af3a40ec0d227b
diff --git a/metadata/md5-cache/sci-biology/kalign-2.03-r2 b/metadata/md5-cache/sci-biology/kalign-2.03-r2
deleted file mode 100644
index e501872fab8c..000000000000
--- a/metadata/md5-cache/sci-biology/kalign-2.03-r2
+++ /dev/null
@@ -1,11 +0,0 @@
-DEFINED_PHASES=compile install prepare
-DESCRIPTION=Global and progressive multiple sequence alignment
-EAPI=6
-HOMEPAGE=http://msa.cgb.ki.se/
-INHERIT=toolchain-funcs
-KEYWORDS=~amd64 ~x86
-LICENSE=GPL-2
-SLOT=0
-SRC_URI=mirror://debian/pool/main/k/kalign/kalign_2.03.orig.tar.gz
-_eclasses_=toolchain-funcs	e9da88162e7a3c60376e80c2c2adcdfb	multilib	4fbbbc98f236f1b43acd99476bc3cd85
-_md5_=175d26382226c7bed2b44be485b01d01
diff --git a/metadata/md5-cache/sci-biology/kalign-2.03-r3 b/metadata/md5-cache/sci-biology/kalign-2.03-r3
new file mode 100644
index 000000000000..1c563dbab5c8
--- /dev/null
+++ b/metadata/md5-cache/sci-biology/kalign-2.03-r3
@@ -0,0 +1,9 @@
+DEFINED_PHASES=-
+DESCRIPTION=Global and progressive multiple sequence alignment
+EAPI=8
+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
+_md5_=6f3350a7a60bf9efddc24e958998f592
diff --git a/metadata/md5-cache/sci-biology/maq-0.7.1-r2 b/metadata/md5-cache/sci-biology/maq-0.7.1-r2
deleted file mode 100644
index 1c34d96b3cca..000000000000
--- a/metadata/md5-cache/sci-biology/maq-0.7.1-r2
+++ /dev/null
@@ -1,13 +0,0 @@
-DEFINED_PHASES=install prepare
-DEPEND=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=Mapping and Assembly with Qualities, mapping NGS reads to reference genomes
-EAPI=6
-HOMEPAGE=http://maq.sourceforge.net/
-INHERIT=autotools
-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_=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_=39ffb0025210075a8d7d7f6f81f8da56
diff --git a/metadata/md5-cache/sci-biology/maq-0.7.1-r3 b/metadata/md5-cache/sci-biology/maq-0.7.1-r3
new file mode 100644
index 000000000000..c10e45bc9b06
--- /dev/null
+++ b/metadata/md5-cache/sci-biology/maq-0.7.1-r3
@@ -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=sys-libs/zlib
+DESCRIPTION=Mapping and Assembly with Qualities, mapping NGS reads to reference genomes
+EAPI=8
+HOMEPAGE=http://maq.sourceforge.net/
+INHERIT=autotools
+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_=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
-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_=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_=dee50558d10e75ff9e96f4c3f177c55f
diff --git a/metadata/md5-cache/sci-biology/maqview-0.2.5-r4 b/metadata/md5-cache/sci-biology/maqview-0.2.5-r4
new file mode 100644
index 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-r2
index 09ab2f9536f6..ead6a9896af6 100644
--- a/metadata/md5-cache/sci-biology/pals-1.0-r1
+++ b/metadata/md5-cache/sci-biology/pals-1.0-r2
@@ -1,6 +1,6 @@
 DEFINED_PHASES=configure install
 DESCRIPTION=Pairwise Aligner for Long Sequences
-EAPI=6
+EAPI=8
 HOMEPAGE=http://www.drive5.com/pals/
 INHERIT=toolchain-funcs
 KEYWORDS=amd64 x86
@@ -8,4 +8,4 @@ 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
+_md5_=0374a4cc1893f560fdb963ab9e27c56b
diff --git a/metadata/md5-cache/sci-biology/phred-071220-r1 b/metadata/md5-cache/sci-biology/phred-071220-r2
index 4f6b8e22eee3..c59c08039029 100644
--- a/metadata/md5-cache/sci-biology/phred-071220-r1
+++ b/metadata/md5-cache/sci-biology/phred-071220-r2
@@ -1,6 +1,6 @@
 DEFINED_PHASES=compile install nofetch
 DESCRIPTION=A base caller for Sanger DNA sequencing
-EAPI=6
+EAPI=8
 HOMEPAGE=http://phrap.org/phredphrapconsed.html
 INHERIT=toolchain-funcs
 KEYWORDS=~amd64 ~x86
@@ -9,4 +9,4 @@ RESTRICT=fetch
 SLOT=0
 SRC_URI=phred-dist-071220.b-acd.tar.gz
 _eclasses_=toolchain-funcs	e9da88162e7a3c60376e80c2c2adcdfb	multilib	4fbbbc98f236f1b43acd99476bc3cd85
-_md5_=6cb07f602eee34da61fd893818f30936
+_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-r4
index 34c540a2e1e2..e4800cea2fcc 100644
--- a/metadata/md5-cache/sci-biology/phyml-2.4.5-r3
+++ b/metadata/md5-cache/sci-biology/phyml-2.4.5-r4
@@ -1,6 +1,6 @@
-DEFINED_PHASES=install prepare
+DEFINED_PHASES=configure install
 DESCRIPTION=Estimation of large phylogenies by maximum likelihood
-EAPI=6
+EAPI=8
 HOMEPAGE=http://atgc.lirmm.fr/phyml/
 INHERIT=toolchain-funcs
 KEYWORDS=amd64 ~ppc x86
@@ -8,4 +8,4 @@ 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
+_md5_=d7f38a7c0005dca5f3da1d1fbd9780ae
diff --git a/metadata/md5-cache/sci-biology/piler-1.0-r1 b/metadata/md5-cache/sci-biology/piler-1.0-r2
index 5641b33a3359..7f660db458c7 100644
--- a/metadata/md5-cache/sci-biology/piler-1.0-r1
+++ b/metadata/md5-cache/sci-biology/piler-1.0-r2
@@ -1,6 +1,6 @@
 DEFINED_PHASES=configure install
 DESCRIPTION=Analysis of repetitive DNA found in genome sequences
-EAPI=6
+EAPI=8
 HOMEPAGE=http://www.drive5.com/piler/
 INHERIT=toolchain-funcs
 KEYWORDS=amd64 x86
@@ -9,4 +9,4 @@ 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
+_md5_=5a8dffca1e2b80e93cf1efdff5fd3fd0
diff --git a/metadata/md5-cache/sci-biology/pilercr-1.0-r1 b/metadata/md5-cache/sci-biology/pilercr-1.0-r2
index c1952ad55f34..140787e0ed04 100644
--- a/metadata/md5-cache/sci-biology/pilercr-1.0-r1
+++ b/metadata/md5-cache/sci-biology/pilercr-1.0-r2
@@ -1,6 +1,6 @@
 DEFINED_PHASES=configure install
 DESCRIPTION=Analysis of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs)
-EAPI=6
+EAPI=8
 HOMEPAGE=http://www.drive5.com/pilercr/
 INHERIT=toolchain-funcs
 KEYWORDS=amd64 x86
@@ -8,4 +8,4 @@ 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
+_md5_=d6fca147863ed9ae98f77d0b6f762060
diff --git a/metadata/md5-cache/sci-biology/prank-140603 b/metadata/md5-cache/sci-biology/prank-140603-r1
index 3951a97f8de1..584c61ad9b18 100644
--- a/metadata/md5-cache/sci-biology/prank-140603
+++ b/metadata/md5-cache/sci-biology/prank-140603-r1
@@ -1,6 +1,6 @@
-DEFINED_PHASES=compile install prepare
+DEFINED_PHASES=configure install
 DESCRIPTION=Probabilistic Alignment Kit
-EAPI=6
+EAPI=8
 HOMEPAGE=http://wasabiapp.org/software/prank/
 INHERIT=toolchain-funcs
 KEYWORDS=~amd64 ~x86
@@ -8,4 +8,4 @@ LICENSE=GPL-3
 SLOT=0
 SRC_URI=http://wasabiapp.org/download/prank/prank.source.140603.tgz
 _eclasses_=toolchain-funcs	e9da88162e7a3c60376e80c2c2adcdfb	multilib	4fbbbc98f236f1b43acd99476bc3cd85
-_md5_=17023476000980284365a9c0ed04a6f0
+_md5_=07f1836dd1c44c4ebf19bb6a59f7141a
diff --git a/metadata/md5-cache/sci-biology/prodigal-2.6.3 b/metadata/md5-cache/sci-biology/prodigal-2.6.3-r1
index ecbdb3a4bb25..1b862f2cfb5b 100644
--- a/metadata/md5-cache/sci-biology/prodigal-2.6.3
+++ b/metadata/md5-cache/sci-biology/prodigal-2.6.3-r1
@@ -1,6 +1,6 @@
 DEFINED_PHASES=configure
 DESCRIPTION=Prokaryotic Dynamic Programming Genefinding Algorithm
-EAPI=6
+EAPI=8
 HOMEPAGE=http://prodigal.ornl.gov/
 INHERIT=toolchain-funcs
 KEYWORDS=~amd64
@@ -8,4 +8,4 @@ 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
+_md5_=fbd84f84d9eeda38c197893cf2c079c8
diff --git a/metadata/md5-cache/sci-biology/recon-1.08 b/metadata/md5-cache/sci-biology/recon-1.08-r1
index 9e9e4eb623bb..6171695c1e65 100644
--- a/metadata/md5-cache/sci-biology/recon-1.08
+++ b/metadata/md5-cache/sci-biology/recon-1.08-r1
@@ -1,6 +1,6 @@
 DEFINED_PHASES=compile install prepare
 DESCRIPTION=Automated de novo identification of repeat families from genomic sequences
-EAPI=6
+EAPI=8
 HOMEPAGE=http://www.repeatmasker.org/RepeatModeler.html
 INHERIT=toolchain-funcs
 IUSE=examples
@@ -10,4 +10,4 @@ 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
+_md5_=36772ec3438da03e296e39fc88b347ee
diff --git a/metadata/md5-cache/sci-biology/rnaview-20040713-r4 b/metadata/md5-cache/sci-biology/rnaview-20040713-r5
index ef7ce4100a57..6d64e471a767 100644
--- a/metadata/md5-cache/sci-biology/rnaview-20040713-r4
+++ b/metadata/md5-cache/sci-biology/rnaview-20040713-r5
@@ -1,6 +1,6 @@
-DEFINED_PHASES=install prepare
+DEFINED_PHASES=configure install
 DESCRIPTION=Generates 2D displays of RNA/DNA secondary structures with tertiary interactions
-EAPI=6
+EAPI=8
 HOMEPAGE=http://ndbserver.rutgers.edu/services/download/index.html
 INHERIT=toolchain-funcs
 KEYWORDS=~amd64 ~x86
@@ -8,4 +8,4 @@ LICENSE=public-domain
 SLOT=0
 SRC_URI=mirror://gentoo/rnaview-20040713.tar.bz2
 _eclasses_=toolchain-funcs	e9da88162e7a3c60376e80c2c2adcdfb	multilib	4fbbbc98f236f1b43acd99476bc3cd85
-_md5_=788c156d45287bef4f6aa876055bde4c
+_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-r3
index 6cec0e77ed2b..c71a62e9c29c 100644
--- a/metadata/md5-cache/sci-biology/t-coffee-11.00-r2
+++ b/metadata/md5-cache/sci-biology/t-coffee-11.00-r3
@@ -1,12 +1,12 @@
-DEFINED_PHASES=compile install prepare
+DEFINED_PHASES=compile configure install
 DESCRIPTION=A multiple sequence alignment package
-EAPI=6
+EAPI=8
 HOMEPAGE=http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html
-INHERIT=toolchain-funcs
+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
-_md5_=5c54b109c5b8bef93adbc5f99ddd7114
+_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-r2
index 91dec5eae8be..4c28d14c7975 100644
--- a/metadata/md5-cache/sci-biology/transfac-3.2-r1
+++ b/metadata/md5-cache/sci-biology/transfac-3.2-r2
@@ -1,7 +1,7 @@
+BDEPEND=emboss? ( sci-biology/emboss )
 DEFINED_PHASES=compile install
-DEPEND=emboss? ( sci-biology/emboss )
 DESCRIPTION=A database of eucaryotic transcription factors
-EAPI=6
+EAPI=8
 HOMEPAGE=http://www.gene-regulation.com/pub/databases.html
 IUSE=emboss minimal
 KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux
@@ -9,4 +9,4 @@ 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
+_md5_=6312c1bc4fc292848eed00fb67efa7c9
diff --git a/metadata/md5-cache/sci-biology/trf-4.04-r1 b/metadata/md5-cache/sci-biology/trf-4.04-r2
index 3195b5c5feec..30e1962524fe 100644
--- a/metadata/md5-cache/sci-biology/trf-4.04-r1
+++ b/metadata/md5-cache/sci-biology/trf-4.04-r2
@@ -1,10 +1,10 @@
 DEFINED_PHASES=install unpack
 DESCRIPTION=Tandem Repeats Finder
-EAPI=6
+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_=51a51c14c6646aaa7d7494d561535729
+_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