6 files changed, 27 insertions, 25 deletions
diff --git a/metadata/md5-cache/sci-biology/Manifest.gz b/metadata/md5-cache/sci-biology/Manifest.gz
index 67ca65a6840b..6739be6faa79 100644
--- a/metadata/md5-cache/sci-biology/Manifest.gz
+++ b/metadata/md5-cache/sci-biology/Manifest.gz
diff --git a/metadata/md5-cache/sci-biology/mrbayes-3.1.2-r2 b/metadata/md5-cache/sci-biology/mrbayes-3.1.2-r2
index 93f28bb858af..e0583c8b4612 100644
--- a/metadata/md5-cache/sci-biology/mrbayes-3.1.2-r2
+++ b/metadata/md5-cache/sci-biology/mrbayes-3.1.2-r2
@@ -1,13 +1,13 @@
 DEFINED_PHASES=compile install prepare
-DEPEND=sys-libs/ncurses:0= mpi? ( virtual/mpi ) readline? ( sys-libs/readline:0= )
+DEPEND=sys-libs/ncurses:= mpi? ( virtual/mpi ) readline? ( sys-libs/readline:= )
 DESCRIPTION=Bayesian Inference of Phylogeny
-EAPI=5
+EAPI=8
 HOMEPAGE=http://mrbayes.csit.fsu.edu/
 IUSE=debug mpi readline
 KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris
 LICENSE=GPL-2
-RDEPEND=sys-libs/ncurses:0= mpi? ( virtual/mpi ) readline? ( sys-libs/readline:0= )
+RDEPEND=sys-libs/ncurses:= mpi? ( virtual/mpi ) readline? ( sys-libs/readline:= )
 SLOT=0
 SRC_URI=mirror://sourceforge/mrbayes/mrbayes-3.1.2.tar.gz
-_eclasses_=epatch	9f813bb3c47cf2e60619a663b87c5f4e	estack	055c42df72f76a4f45ec92b35e83cd56	multilib	97566c1a256d07b00848aa767e38a352	toolchain-funcs	9ea1c67b6f8315fdc2568abb674519aa
-_md5_=c97a54ea522e76af98a9b4e7e29e79cc
+_eclasses_=multilib	97566c1a256d07b00848aa767e38a352	toolchain-funcs	9ea1c67b6f8315fdc2568abb674519aa
+_md5_=934b64005f56b5809a9cbbdf69aab63b
diff --git a/metadata/md5-cache/sci-biology/plink-1.90_pre140514 b/metadata/md5-cache/sci-biology/plink-1.90_pre140514
index 4b0c15f37118..f9630e2f016b 100644
--- a/metadata/md5-cache/sci-biology/plink-1.90_pre140514
+++ b/metadata/md5-cache/sci-biology/plink-1.90_pre140514
@@ -1,7 +1,8 @@
+BDEPEND=app-arch/unzip virtual/pkgconfig
 DEFINED_PHASES=compile install prepare
-DEPEND=sys-libs/zlib virtual/cblas virtual/lapack app-arch/unzip virtual/pkgconfig
+DEPEND=sys-libs/zlib virtual/cblas virtual/lapack
 DESCRIPTION=Whole genome association analysis toolset
-EAPI=5
+EAPI=8
 HOMEPAGE=http://pngu.mgh.harvard.edu/~purcell/plink/
 KEYWORDS=~amd64 ~x86
 LICENSE=GPL-2
@@ -9,4 +10,4 @@ RDEPEND=sys-libs/zlib virtual/cblas virtual/lapack
 SLOT=0
 SRC_URI=http://pngu.mgh.harvard.edu/~purcell/static/bin/plink140514/plink_src.zip -> plink-1.90_pre140514.zip
 _eclasses_=multilib	97566c1a256d07b00848aa767e38a352	toolchain-funcs	9ea1c67b6f8315fdc2568abb674519aa
-_md5_=e1f50da3f99cd26238e4ef37a7de379a
+_md5_=e839f5daef081dde4b2d3e0417010738
diff --git a/metadata/md5-cache/sci-biology/velvet-1.2.10 b/metadata/md5-cache/sci-biology/velvet-1.2.10
index eec750f367f6..6f71b25cdea9 100644
--- a/metadata/md5-cache/sci-biology/velvet-1.2.10
+++ b/metadata/md5-cache/sci-biology/velvet-1.2.10
@@ -1,12 +1,12 @@
+BDEPEND=doc? ( virtual/latex-base )
 DEFINED_PHASES=compile install prepare test
-DEPEND=doc? ( virtual/latex-base )
 DESCRIPTION=A sequence assembler for very short reads
-EAPI=5
+EAPI=8
 HOMEPAGE=https://www.ebi.ac.uk/~zerbino/velvet/
 IUSE=doc openmp
 KEYWORDS=~amd64 ~x86
 LICENSE=GPL-2
 SLOT=0
 SRC_URI=https://www.ebi.ac.uk/~zerbino/velvet/velvet_1.2.10.tgz
-_eclasses_=desktop	c0d27bf73aa08ca05b663dbd31fbef28	edos2unix	33e347e171066657f91f8b0c72ec8773	epatch	9f813bb3c47cf2e60619a663b87c5f4e	estack	055c42df72f76a4f45ec92b35e83cd56	eutils	dab5d8ec471d025b79c9e6906bcf3bff	flag-o-matic	4134b5c0fb719b9161d10bdaba9e09e5	ltprune	4f3f2db5ce3ccbeeacdf3f94954043aa	multilib	97566c1a256d07b00848aa767e38a352	preserve-libs	dbc9f8d2d49c66467bc327fddd8317bd	strip-linguas	ac3ee41ee2d31d8c41a77c0838320cc7	toolchain-funcs	9ea1c67b6f8315fdc2568abb674519aa	vcs-clean	b690a7e9b6c497cf59326a7545df4283	wrapper	4251d4c84c25f59094fd557e0063a974
-_md5_=b07b48444158719f00b415b6f8b8e6a1
+_eclasses_=flag-o-matic	4134b5c0fb719b9161d10bdaba9e09e5	multilib	97566c1a256d07b00848aa767e38a352	toolchain-funcs	9ea1c67b6f8315fdc2568abb674519aa
+_md5_=f48eb0348a1ac91d41dde22d3ced2ea1
diff --git a/metadata/md5-cache/sci-biology/wise-2.4.0_alpha b/metadata/md5-cache/sci-biology/wise-2.4.0_alpha
deleted file mode 100644
index 173af71c9d6d..000000000000
--- a/metadata/md5-cache/sci-biology/wise-2.4.0_alpha
+++ /dev/null
@@ -1,13 +0,0 @@
-DEFINED_PHASES=compile install prepare test
-DEPEND=~sci-biology/hmmer-2.3.2 app-shells/tcsh dev-lang/perl virtual/latex-base
-DESCRIPTION=Intelligent algorithms for DNA searches
-EAPI=5
-HOMEPAGE=http://www.ebi.ac.uk/Wise2/
-IUSE=doc static-libs
-KEYWORDS=~amd64 ~x86
-LICENSE=BSD
-RDEPEND=~sci-biology/hmmer-2.3.2
-SLOT=0
-SRC_URI=ftp://ftp.ebi.ac.uk/pub/software/wise2/wise2.4.0alpha.tar.gz https://dev.gentoo.org/~mgorny/dist/wise-2.4.0_alpha-patchset.tar.bz2
-_eclasses_=epatch	9f813bb3c47cf2e60619a663b87c5f4e	estack	055c42df72f76a4f45ec92b35e83cd56	multilib	97566c1a256d07b00848aa767e38a352	toolchain-funcs	9ea1c67b6f8315fdc2568abb674519aa	versionator	d3fb3ba33acc3bbbdc4d7970227c100d
-_md5_=d5566134a062c60e1c2223a1b1283862
diff --git a/metadata/md5-cache/sci-biology/wise-2.4.0_alpha-r1 b/metadata/md5-cache/sci-biology/wise-2.4.0_alpha-r1
new file mode 100644
index 000000000000..31ec4dfd8d82
--- /dev/null
+++ b/metadata/md5-cache/sci-biology/wise-2.4.0_alpha-r1
@@ -0,0 +1,14 @@
+BDEPEND=app-shells/tcsh dev-lang/perl virtual/latex-base
+DEFINED_PHASES=compile install prepare test
+DEPEND=~sci-biology/hmmer-2.3.2
+DESCRIPTION=Intelligent algorithms for DNA searches
+EAPI=8
+HOMEPAGE=http://www.ebi.ac.uk/Wise2/
+IUSE=doc
+KEYWORDS=~amd64 ~x86
+LICENSE=BSD
+RDEPEND=~sci-biology/hmmer-2.3.2
+SLOT=0
+SRC_URI=ftp://ftp.ebi.ac.uk/pub/software/wise2/wise2.4.0alpha.tar.gz https://dev.gentoo.org/~mgorny/dist/wise-2.4.0_alpha-patchset.tar.bz2
+_eclasses_=multilib	97566c1a256d07b00848aa767e38a352	toolchain-funcs	9ea1c67b6f8315fdc2568abb674519aa
+_md5_=34f9a1f8b8f239e402200b9b5cb4f3cc