2018-05-21 17:30:40 UTC

12 files changed, 29 insertions, 42 deletions

diff --git a/metadata/md5-cache/sci-biology/fasta-36.3.5e b/metadata/md5-cache/sci-biology/fasta-36.3.5e
index c84e5f5e6288..85cbd3251d6d 100644
--- a/metadata/md5-cache/sci-biology/fasta-36.3.5e
+++ b/metadata/md5-cache/sci-biology/fasta-36.3.5e
@@ -2,11 +2,11 @@ DEFINED_PHASES=compile install prepare test
 DEPEND=test? ( app-shells/tcsh )
 DESCRIPTION=FASTA is a DNA and Protein sequence alignment software package
 EAPI=5
-HOMEPAGE=http://fasta.bioch.virginia.edu/fasta_www2/fasta_down.shtml
+HOMEPAGE=https://fasta.bioch.virginia.edu/fasta_www2/fasta_down.shtml
 IUSE=debug cpu_flags_x86_sse2 test
 KEYWORDS=~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos
 LICENSE=fasta
 SLOT=0
 SRC_URI=http://faculty.virginia.edu/wrpearson/fasta/fasta36/fasta-36.3.5e.tar.gz
 _eclasses_=desktop	2ccd1dd1dd7bfb8795eea024a4f91bb6	epatch	9a5f039771f143195164a15a4faa41a1	estack	43ddf5aaffa7a8d0482df54d25a66a1f	eutils	63392afb034aad67f17fa129019eb4d9	flag-o-matic	5128c4729303400bd8d4b0b966530955	ltprune	607e058da37aa6dabfa408b7d61da72e	multilib	97f470f374f2e94ccab04a2fb21d811e	preserve-libs	ef207dc62baddfddfd39a164d9797648	toolchain-funcs	fa02994d0beba88681127d93da4411ec	vcs-clean	2a0f74a496fa2b1552c4f3398258b7bf
-_md5_=7b46f81d2659e9120c49874e774b5ca0
+_md5_=4eed9011a4fc400bdf3adf77be6c8fe2
diff --git a/metadata/md5-cache/sci-biology/glimmer-3.02-r3 b/metadata/md5-cache/sci-biology/glimmer-3.02-r3
index 843dc56f0e06..1b6d7971fa45 100644
--- a/metadata/md5-cache/sci-biology/glimmer-3.02-r3
+++ b/metadata/md5-cache/sci-biology/glimmer-3.02-r3
@@ -1,11 +1,11 @@
 DEFINED_PHASES=compile install prepare
 DESCRIPTION=An HMM-based microbial gene finding system from TIGR
 EAPI=5
-HOMEPAGE=http://www.cbcb.umd.edu/software/glimmer/
+HOMEPAGE=https://ccb.jhu.edu/software/glimmer/index.shtml
 KEYWORDS=amd64 x86
 LICENSE=Artistic
 RDEPEND=app-shells/tcsh
 SLOT=0
 SRC_URI=http://www.cbcb.umd.edu/software/glimmer/glimmer302.tar.gz
 _eclasses_=desktop	2ccd1dd1dd7bfb8795eea024a4f91bb6	epatch	9a5f039771f143195164a15a4faa41a1	estack	43ddf5aaffa7a8d0482df54d25a66a1f	eutils	63392afb034aad67f17fa129019eb4d9	ltprune	607e058da37aa6dabfa408b7d61da72e	multilib	97f470f374f2e94ccab04a2fb21d811e	preserve-libs	ef207dc62baddfddfd39a164d9797648	toolchain-funcs	fa02994d0beba88681127d93da4411ec	vcs-clean	2a0f74a496fa2b1552c4f3398258b7bf
-_md5_=fda3f095f34da47d12e170b3c40dfd67
+_md5_=94600a4de5a2dc02bc6652d958a2a034
diff --git a/metadata/md5-cache/sci-biology/glimmer-3.02b b/metadata/md5-cache/sci-biology/glimmer-3.02b
index e4223fafef93..f143f44f0657 100644
--- a/metadata/md5-cache/sci-biology/glimmer-3.02b
+++ b/metadata/md5-cache/sci-biology/glimmer-3.02b
@@ -1,11 +1,11 @@
 DEFINED_PHASES=compile install prepare
 DESCRIPTION=An HMM-based microbial gene finding system from TIGR
 EAPI=5
-HOMEPAGE=http://ccb.jhu.edu/software/glimmer
+HOMEPAGE=https://ccb.jhu.edu/software/glimmer/index.shtml
 KEYWORDS=~amd64 ~x86
 LICENSE=Artistic
 RDEPEND=app-shells/tcsh sci-biology/elph
 SLOT=0
-SRC_URI=http://ccb.jhu.edu/software/glimmer/glimmer302b.tar.gz
+SRC_URI=https://ccb.jhu.edu/software/glimmer/glimmer302b.tar.gz
 _eclasses_=desktop	2ccd1dd1dd7bfb8795eea024a4f91bb6	epatch	9a5f039771f143195164a15a4faa41a1	estack	43ddf5aaffa7a8d0482df54d25a66a1f	eutils	63392afb034aad67f17fa129019eb4d9	ltprune	607e058da37aa6dabfa408b7d61da72e	multilib	97f470f374f2e94ccab04a2fb21d811e	preserve-libs	ef207dc62baddfddfd39a164d9797648	toolchain-funcs	fa02994d0beba88681127d93da4411ec	vcs-clean	2a0f74a496fa2b1552c4f3398258b7bf
-_md5_=1a77df881e0fba38094c344e97b529a5
+_md5_=6916d92c69198563f19b744f1e57dddc
diff --git a/metadata/md5-cache/sci-biology/mafft-7.050 b/metadata/md5-cache/sci-biology/mafft-7.050
index 43c9ceb9f18a..d291ae40be8d 100644
--- a/metadata/md5-cache/sci-biology/mafft-7.050
+++ b/metadata/md5-cache/sci-biology/mafft-7.050
@@ -1,11 +1,11 @@
 DEFINED_PHASES=compile install prepare test
 DESCRIPTION=Multiple sequence alignments using a variety of algorithms
 EAPI=5
-HOMEPAGE=http://mafft.cbrc.jp/alignment/software/index.html
+HOMEPAGE=https://mafft.cbrc.jp/alignment/software/index.html
 IUSE=threads
 KEYWORDS=amd64 x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos
 LICENSE=BSD
 SLOT=0
-SRC_URI=http://mafft.cbrc.jp/alignment/software/mafft-7.050-without-extensions-src.tgz
+SRC_URI=https://mafft.cbrc.jp/alignment/software/mafft-7.050-without-extensions-src.tgz
 _eclasses_=desktop	2ccd1dd1dd7bfb8795eea024a4f91bb6	epatch	9a5f039771f143195164a15a4faa41a1	estack	43ddf5aaffa7a8d0482df54d25a66a1f	eutils	63392afb034aad67f17fa129019eb4d9	flag-o-matic	5128c4729303400bd8d4b0b966530955	ltprune	607e058da37aa6dabfa408b7d61da72e	multilib	97f470f374f2e94ccab04a2fb21d811e	preserve-libs	ef207dc62baddfddfd39a164d9797648	toolchain-funcs	fa02994d0beba88681127d93da4411ec	vcs-clean	2a0f74a496fa2b1552c4f3398258b7bf
-_md5_=10435da51da43a9bd92e9e337fb92445
+_md5_=3195e77c5c792018208b65f5dbeab567
diff --git a/metadata/md5-cache/sci-biology/mafft-7.215 b/metadata/md5-cache/sci-biology/mafft-7.215
index b3056161a6a3..ca1eceb71b49 100644
--- a/metadata/md5-cache/sci-biology/mafft-7.215
+++ b/metadata/md5-cache/sci-biology/mafft-7.215
@@ -1,11 +1,11 @@
 DEFINED_PHASES=compile install prepare test
 DESCRIPTION=Multiple sequence alignments using a variety of algorithms
 EAPI=5
-HOMEPAGE=http://mafft.cbrc.jp/alignment/software/index.html
+HOMEPAGE=https://mafft.cbrc.jp/alignment/software/index.html
 IUSE=threads
 KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos
 LICENSE=BSD
 SLOT=0
-SRC_URI=http://mafft.cbrc.jp/alignment/software/mafft-7.215-without-extensions-src.tgz
+SRC_URI=https://mafft.cbrc.jp/alignment/software/mafft-7.215-without-extensions-src.tgz
 _eclasses_=desktop	2ccd1dd1dd7bfb8795eea024a4f91bb6	epatch	9a5f039771f143195164a15a4faa41a1	estack	43ddf5aaffa7a8d0482df54d25a66a1f	eutils	63392afb034aad67f17fa129019eb4d9	flag-o-matic	5128c4729303400bd8d4b0b966530955	ltprune	607e058da37aa6dabfa408b7d61da72e	multilib	97f470f374f2e94ccab04a2fb21d811e	preserve-libs	ef207dc62baddfddfd39a164d9797648	toolchain-funcs	fa02994d0beba88681127d93da4411ec	vcs-clean	2a0f74a496fa2b1552c4f3398258b7bf
-_md5_=26a81f4b6b0ff69fbc3eba8869681491
+_md5_=7b8b136195c000efff0407f671d57f19
diff --git a/metadata/md5-cache/sci-biology/mafft-7.305 b/metadata/md5-cache/sci-biology/mafft-7.305
index 29a6530ae474..79313944ef91 100644
--- a/metadata/md5-cache/sci-biology/mafft-7.305
+++ b/metadata/md5-cache/sci-biology/mafft-7.305
@@ -1,11 +1,11 @@
 DEFINED_PHASES=compile install prepare test
 DESCRIPTION=Multiple sequence alignments using a variety of algorithms
 EAPI=6
-HOMEPAGE=http://mafft.cbrc.jp/alignment/software/index.html
+HOMEPAGE=https://mafft.cbrc.jp/alignment/software/index.html
 IUSE=threads
 KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos
 LICENSE=BSD
 SLOT=0
-SRC_URI=http://mafft.cbrc.jp/alignment/software/mafft-7.305-without-extensions-src.tgz
+SRC_URI=https://mafft.cbrc.jp/alignment/software/mafft-7.305-without-extensions-src.tgz
 _eclasses_=desktop	2ccd1dd1dd7bfb8795eea024a4f91bb6	epatch	9a5f039771f143195164a15a4faa41a1	estack	43ddf5aaffa7a8d0482df54d25a66a1f	eutils	63392afb034aad67f17fa129019eb4d9	flag-o-matic	5128c4729303400bd8d4b0b966530955	ltprune	607e058da37aa6dabfa408b7d61da72e	multilib	97f470f374f2e94ccab04a2fb21d811e	preserve-libs	ef207dc62baddfddfd39a164d9797648	toolchain-funcs	fa02994d0beba88681127d93da4411ec	vcs-clean	2a0f74a496fa2b1552c4f3398258b7bf
-_md5_=4701ed0cbf5fff28c6de7c8b01e134af
+_md5_=920a37021a0b392bb7315b63cf3de39d
diff --git a/metadata/md5-cache/sci-biology/mothur-1.27.0-r1 b/metadata/md5-cache/sci-biology/mothur-1.27.0-r1
index 4abca291abd7..391a0eb6ed12 100644
--- a/metadata/md5-cache/sci-biology/mothur-1.27.0-r1
+++ b/metadata/md5-cache/sci-biology/mothur-1.27.0-r1
@@ -2,12 +2,12 @@ DEFINED_PHASES=compile install prepare setup
 DEPEND=sci-biology/uchime mpi? ( virtual/mpi ) app-arch/unzip virtual/fortran
 DESCRIPTION=A suite of algorithms for ecological bioinformatics
 EAPI=5
-HOMEPAGE=http://www.mothur.org/
+HOMEPAGE=https://www.mothur.org/
 IUSE=mpi +readline
 KEYWORDS=amd64 x86
 LICENSE=GPL-3
 RDEPEND=sci-biology/uchime mpi? ( virtual/mpi ) virtual/fortran
 SLOT=0
-SRC_URI=http://www.mothur.org/w/images/c/cb/Mothur.1.27.0.zip -> mothur-1.27.0.zip
+SRC_URI=https://www.mothur.org/w/images/c/cb/Mothur.1.27.0.zip -> mothur-1.27.0.zip
 _eclasses_=desktop	2ccd1dd1dd7bfb8795eea024a4f91bb6	epatch	9a5f039771f143195164a15a4faa41a1	estack	43ddf5aaffa7a8d0482df54d25a66a1f	eutils	63392afb034aad67f17fa129019eb4d9	flag-o-matic	5128c4729303400bd8d4b0b966530955	fortran-2	9e7f20c99213f0627ff7f873d4aaa25d	ltprune	607e058da37aa6dabfa408b7d61da72e	multilib	97f470f374f2e94ccab04a2fb21d811e	preserve-libs	ef207dc62baddfddfd39a164d9797648	toolchain-funcs	fa02994d0beba88681127d93da4411ec	vcs-clean	2a0f74a496fa2b1552c4f3398258b7bf
-_md5_=abcc03749068210ba5c44ba0b4a85e27
+_md5_=17f8b3c73710bbb746fc4cbfcf78b85d
diff --git a/metadata/md5-cache/sci-biology/ncbi-tools-2.2.26-r2 b/metadata/md5-cache/sci-biology/ncbi-tools-2.2.26-r2
index 157ec8d46fbd..8f2eda2fc6ba 100644
--- a/metadata/md5-cache/sci-biology/ncbi-tools-2.2.26-r2
+++ b/metadata/md5-cache/sci-biology/ncbi-tools-2.2.26-r2
@@ -2,7 +2,7 @@ DEFINED_PHASES=compile install prepare setup
 DEPEND=app-shells/tcsh dev-lang/perl media-libs/libpng:0= X? ( media-libs/fontconfig x11-libs/motif:0= x11-libs/libICE x11-libs/libX11 x11-libs/libXft x11-libs/libXmu x11-libs/libXt )
 DESCRIPTION=Development toolkit and applications for computational biology, including BLAST
 EAPI=5
-HOMEPAGE=http://www.ncbi.nlm.nih.gov/
+HOMEPAGE=https://www.ncbi.nlm.nih.gov/
 IUSE=doc static-libs X
 KEYWORDS=~alpha amd64 ppc64 x86 ~amd64-linux ~x86-linux ~ppc-macos
 LICENSE=public-domain
@@ -10,4 +10,4 @@ RDEPEND=app-shells/tcsh dev-lang/perl media-libs/libpng:0= X? ( media-libs/fontc
 SLOT=0
 SRC_URI=ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/2.2.26/ncbi.tar.gz -> ncbi-tools-2.2.26.tar.gz
 _eclasses_=desktop	2ccd1dd1dd7bfb8795eea024a4f91bb6	epatch	9a5f039771f143195164a15a4faa41a1	estack	43ddf5aaffa7a8d0482df54d25a66a1f	eutils	63392afb034aad67f17fa129019eb4d9	flag-o-matic	5128c4729303400bd8d4b0b966530955	ltprune	607e058da37aa6dabfa408b7d61da72e	multilib	97f470f374f2e94ccab04a2fb21d811e	prefix	e51c7882b7b721e54e684f7eb143cbfe	preserve-libs	ef207dc62baddfddfd39a164d9797648	toolchain-funcs	fa02994d0beba88681127d93da4411ec	vcs-clean	2a0f74a496fa2b1552c4f3398258b7bf
-_md5_=770169ddfbcde7c5fbe57bff9b10ca14
+_md5_=550e2f5b19e400b1ca82a7ba4f7bd44a
diff --git a/metadata/md5-cache/sci-biology/prosite-2017.02 b/metadata/md5-cache/sci-biology/prosite-2017.02
index 628597305894..ccabbc4a37bb 100644
--- a/metadata/md5-cache/sci-biology/prosite-2017.02
+++ b/metadata/md5-cache/sci-biology/prosite-2017.02
@@ -2,11 +2,11 @@ DEFINED_PHASES=compile install
 DEPEND=emboss? ( sci-biology/emboss )
 DESCRIPTION=A protein families and domains database
 EAPI=6
-HOMEPAGE=http://prosite.expasy.org/
+HOMEPAGE=https://prosite.expasy.org/
 IUSE=emboss minimal
 KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux
 LICENSE=swiss-prot
 RDEPEND=emboss? ( sci-biology/emboss )
 SLOT=0
 SRC_URI=ftp://ftp.expasy.org/databases/prosite/old_releases/prosite2017_02.tar.bz2
-_md5_=390ff0ea61f44c9ea889684cad12b2b2
+_md5_=e37bd9f81e9458715d22a6138fb2029a
diff --git a/metadata/md5-cache/sci-biology/velvet-1.0.18-r1 b/metadata/md5-cache/sci-biology/velvet-1.0.18-r1
index 3c4506c95ab9..3c289ffee6bc 100644
--- a/metadata/md5-cache/sci-biology/velvet-1.0.18-r1
+++ b/metadata/md5-cache/sci-biology/velvet-1.0.18-r1
@@ -2,12 +2,12 @@ DEFINED_PHASES=compile install postinst prepare
 DEPEND=sys-libs/zlib doc? ( virtual/latex-base )
 DESCRIPTION=A sequence assembler for very short reads
 EAPI=4
-HOMEPAGE=http://www.ebi.ac.uk/~zerbino/velvet/
+HOMEPAGE=https://www.ebi.ac.uk/~zerbino/velvet/
 IUSE=-doc
 KEYWORDS=amd64 x86
 LICENSE=GPL-2
 RDEPEND=sys-libs/zlib
 SLOT=0
-SRC_URI=http://www.ebi.ac.uk/~zerbino/velvet/velvet_1.0.18.tgz
+SRC_URI=https://www.ebi.ac.uk/~zerbino/velvet/velvet_1.0.18.tgz
 _eclasses_=desktop	2ccd1dd1dd7bfb8795eea024a4f91bb6	epatch	9a5f039771f143195164a15a4faa41a1	estack	43ddf5aaffa7a8d0482df54d25a66a1f	eutils	63392afb034aad67f17fa129019eb4d9	flag-o-matic	5128c4729303400bd8d4b0b966530955	ltprune	607e058da37aa6dabfa408b7d61da72e	multilib	97f470f374f2e94ccab04a2fb21d811e	preserve-libs	ef207dc62baddfddfd39a164d9797648	toolchain-funcs	fa02994d0beba88681127d93da4411ec	vcs-clean	2a0f74a496fa2b1552c4f3398258b7bf
-_md5_=89c605a4c416ef8207f85201e0494734
+_md5_=81d9bd82f6f3df3f4b73fa7d65b5d95e
diff --git a/metadata/md5-cache/sci-biology/velvet-1.2.10 b/metadata/md5-cache/sci-biology/velvet-1.2.10
index 49295e1e9891..b20c1caf8057 100644
--- a/metadata/md5-cache/sci-biology/velvet-1.2.10
+++ b/metadata/md5-cache/sci-biology/velvet-1.2.10
@@ -2,11 +2,11 @@ DEFINED_PHASES=compile install prepare test
 DEPEND=doc? ( virtual/latex-base )
 DESCRIPTION=A sequence assembler for very short reads
 EAPI=5
-HOMEPAGE=http://www.ebi.ac.uk/~zerbino/velvet/
+HOMEPAGE=https://www.ebi.ac.uk/~zerbino/velvet/
 IUSE=doc openmp
 KEYWORDS=~amd64 ~x86
 LICENSE=GPL-2
 SLOT=0
-SRC_URI=http://www.ebi.ac.uk/~zerbino/velvet/velvet_1.2.10.tgz
+SRC_URI=https://www.ebi.ac.uk/~zerbino/velvet/velvet_1.2.10.tgz
 _eclasses_=desktop	2ccd1dd1dd7bfb8795eea024a4f91bb6	epatch	9a5f039771f143195164a15a4faa41a1	estack	43ddf5aaffa7a8d0482df54d25a66a1f	eutils	63392afb034aad67f17fa129019eb4d9	flag-o-matic	5128c4729303400bd8d4b0b966530955	ltprune	607e058da37aa6dabfa408b7d61da72e	multilib	97f470f374f2e94ccab04a2fb21d811e	preserve-libs	ef207dc62baddfddfd39a164d9797648	toolchain-funcs	fa02994d0beba88681127d93da4411ec	vcs-clean	2a0f74a496fa2b1552c4f3398258b7bf
-_md5_=b46e328f5bece618fd1f41cde92b68c0
+_md5_=420632435bf1efe77241192fff993a20
diff --git a/metadata/md5-cache/sci-biology/wgs-assembler-7.0-r1 b/metadata/md5-cache/sci-biology/wgs-assembler-7.0-r1
deleted file mode 100644
index 9d697077c990..000000000000
--- a/metadata/md5-cache/sci-biology/wgs-assembler-7.0-r1
+++ /dev/null
@@ -1,13 +0,0 @@
-DEFINED_PHASES=compile configure install prepare
-DEPEND=x11-libs/libXt !x11-terms/terminator
-DESCRIPTION=The Celera de novo whole-genome shotgun DNA sequence assembler, aka CABOG
-EAPI=4
-HOMEPAGE=https://sourceforge.net/projects/wgs-assembler/
-IUSE=static-libs
-KEYWORDS=amd64 x86
-LICENSE=GPL-2
-RDEPEND=x11-libs/libXt !x11-terms/terminator app-shells/tcsh dev-perl/Log-Log4perl
-SLOT=0
-SRC_URI=mirror://sourceforge/wgs-assembler/wgs-7.0.tar.bz2
-_eclasses_=desktop	2ccd1dd1dd7bfb8795eea024a4f91bb6	epatch	9a5f039771f143195164a15a4faa41a1	estack	43ddf5aaffa7a8d0482df54d25a66a1f	eutils	63392afb034aad67f17fa129019eb4d9	ltprune	607e058da37aa6dabfa408b7d61da72e	multilib	97f470f374f2e94ccab04a2fb21d811e	preserve-libs	ef207dc62baddfddfd39a164d9797648	toolchain-funcs	fa02994d0beba88681127d93da4411ec	vcs-clean	2a0f74a496fa2b1552c4f3398258b7bf
-_md5_=6ebc94c9eb0083edd0308af8a336afe0