Hash: SHA512
AUX 6.811-respect.patch 6327 SHA256 3d527220ce3fb90e4fa2dd2f41bca1f2684bb03f0de94313d7aea432b955e37c SHA512 0e7e829cc95fcf218fbdf9763983ee6d6ecfb6153201c302fb18ef05818ee19b3b7852c1f85162d2eb2055869033f759cdb3fdbc98cfe4d30ee3607148290e6c WHIRLPOOL ae5c596613dab72df381f849cff927a44dd7f1d9281564fa51f019f38e7435175293674390418f19bbd7305fe4a4748db87abd83cc49a67954ae2a05a6747efb
-AUX mafft-6.240-mktemp.patch 6497 SHA256 783f6f5678781dff1fafece92f37688698052fe1e0bfa13850443a0f8cc91533 SHA512 ade9d0f296a70324f4847763d03585b29cea6bd4a81fa04868eb92df56da40f9df0877f9b310de925c257baaac50208ca17f406639a87cd10c2c83361463b571 WHIRLPOOL af88a170882c110e44026f3402a8d1192264865e1f028725eb1d4d3e94bf7793c4190c53437d1e29e3a57d29e4e08cf8c10db517641f2c809c862a300a27ef0e
AUX mafft-7.037-respect.patch 7463 SHA256 eeedc574ad5977661ea879eefaa1c4b4d428384f25af891c1fcef16e6bfc6293 SHA512 ba706bc83b1c249c08fa7e39d6b80df42be058ea2e68baf1028125dcad289764ead3a6269e557bffc62da87a7ac2ff9856a602e20ca5eae052060d44b431994b WHIRLPOOL cf340ae92dec7ac35099706e5f2a31ac123b341391d2ebe25d4050fc470bbc295ab51c26612c4cc6c659abfba48c355df170b5352b2a6b6a04e8eeca6f453bb5
DIST mafft-7.050-without-extensions-src.tgz 380375 SHA256 29ddb276bfca24f5815acc41f1e640a705bb12c9d29b7c74902ebca68cece7bc SHA512 ffddedcd03f37241b1493a62bf843eb23caa04089bd0182006aa7669f74de27204d324817e22fec1cb4ae11c4c226db5b725d03ba9f73b30a71ca3d38368d73e WHIRLPOOL d46d7d4dfe453bfb54b9e418308772fb063bffce1d6d45d92262bee45504301daff9a6e57ecde41912a6c11852bb64510fb5ba6df04c7e79dc671e7a31444d49
+DIST mafft-7.215-without-extensions-src.tgz 393239 SHA256 22099e42274ef0078302d7cb87180880ee5fd64ef15fdcafd8c95d0018191408 SHA512 1a44b968e2f9ac9db5d17487163a38a7138dc784e63b3aa4082ff6a16c8e168edd09948e2cf182bc7a466802d4a07bdd7ab23386e251df13520acdfb69ebdada WHIRLPOOL de43ba4107e3c1149d5ce47085bacc996393a7ef73535777439b7024eea1dce5f28c1b3c7e518f644345b7b5ea5e70fccbcaba18f16ecb9a6f5f5c31a6b5dca4
EBUILD mafft-7.050.ebuild 1905 SHA256 3949ee9a5a0c3f006a55911db257bf76021d771b22caaac5fed5c3d75db1d145 SHA512 5cf23b2f11c0d1fae8e9b6f8856a7a315594fa6d2318cebf347493e7f002035a98a4a86ea49b5b837f94eb85fc514ca895986c007c98fbf8f99fcf8461ef9f45 WHIRLPOOL ffccf95094ec7c59ffd3ef56f43486d1cfe9c1fa809e201605207880e33d6dc9284b69dfd806ac54ec4634534cd77ee6818c476275b51c6956172a083da242d4
-MISC ChangeLog 3520 SHA256 5ae483fbb76656a462c030b0a09def7b9ee090607a03170175afe1bf202d6792 SHA512 b5839a9ada230f6a09c5128e3daca7850cef455b97b88a20cc6279b4c4d54d8e29444a7b7909eb8476fe558da642d9ede4b7d125c0baa5767be5c998e5db1fb2 WHIRLPOOL 0ce7d9f45df107addac0ab0dfb34b45c1968c76f88c5f955987c2fe8845af1b02464bd1fe111a1c04efa1d48f135712c71ee725f152c9da8b7a007a7cf1cecce
+EBUILD mafft-7.215.ebuild 2083 SHA256 c52113c6a652fa5ce1e1bb58d50ac0323e26084bc185fb0905b115083d2f0bcc SHA512 8c8a2a86a801d6745bca54c93dd60ff006a554d69923c05272d075cda3cbe7241a0ca4a2111c5a1f633d2a6df58ca295e136585830565f1131732ac30c5e7971 WHIRLPOOL c204abaa673a374147891931f2b541cb08e93ffe50a4c94f103ca8a8849e9927ea891448300f2cab9be21a6e6931ee148a5ff8f1e801322e846c0fc7c8a471ba
+MISC ChangeLog 3687 SHA256 1f62a5d8784408af9aeefa03fa7b03bc8fa07c1ad552bf0a36e91fe6cb3378e9 SHA512 f1ec6859e657ad67b5ae61b23910cf564077cfc8d837474ce6fffa0199a523c219be123cbeb260c80c73c8bbe11e7d478764865ff2562469a8110d724cf84f45 WHIRLPOOL 6e1ef4419c83a38d7c36176b06a3ae376e2b318edfbca35c8d5dd59c1f9df70a2b6fd962eaf3a92f5ebb9c7aef621efff222c23b64f70b4a5fc06593e0902162
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-diff -Naur mafft-6.240/src/mafft-homologs.tmpl mafft-6.240.new/src/mafft-homologs.tmpl
---- mafft-6.240/src/mafft-homologs.tmpl 2006-10-01 20:31:38.000000000 -0400
-+++ mafft-6.240.new/src/mafft-homologs.tmpl 2008-09-05 17:14:17.000000000 -0400
-@@ -31,11 +31,22 @@
- # -w entire sequences are subjected to BLAST search
- # (default: well-aligned region only)
-
--
- require 'getopts'
-+require 'tempfile'
-+
-+# create temporary files
-+temp_vf = Tempfile.new("_vf").path
-+temp_if = Tempfile.new("_if").path
-+temp_pf = Tempfile.new("_pf").path
-+temp_af = Tempfile.new("_af").path
-+temp_qf = Tempfile.new("_qf").path
-+temp_bf = Tempfile.new("_bf").path
-+temp_rid = Tempfile.new("_rid").path
-+temp_res = Tempfile.new("_res").path
-
--system( mafftpath + " --help > /tmp/_vf#{$$} 2>&1" )
--pfp = File.open( "/tmp/_vf#{$$}", 'r' )
-+
-+system( mafftpath + " --help > #{temp_vf} 2>&1" )
-+pfp = File.open( "#{temp_vf}", 'r' )
- while pfp.gets
- break if $_ =~ /MAFFT v/
- end
-@@ -114,35 +125,38 @@
- mafftopt += " " + $OPT_o + " "
- end
-
--system "cat " + ARGV.to_s + " > /tmp/_if#{$$}"
-+system "cat " + ARGV.to_s + " > #{temp_if}"
- ar = mafftopt.split(" ")
- nar = ar.length
- for i in 0..(nar-1)
- if ar[i] == "--seed" then
-- system "cat #{ar[i+1]} >> /tmp/_if#{$$}"
-+ system "cat #{ar[i+1]} >> #{temp_if}"
- end
- end
-
- nseq = 0
--ifp = File.open( "/tmp/_if#{$$}", 'r' )
-+ifp = File.open( "#{temp_if}", 'r' )
- while ifp.gets
- nseq += 1 if $_ =~ /^>/
- end
- ifp.close
-
--STDERR.puts "Performing preliminary alignment .. "
--if nseq == 1 then
-- system( "cp /tmp/_if#{$$}" + " /tmp/_pf#{$$}" )
-+if nseq >= 100 then
-+ STDERR.puts "The number of input sequences must be <100."
-+ exit
-+elsif nseq == 1 then
-+ system( "cp #{temp_if}" + " #{temp_pf}" )
- else
-+ STDERR.puts "Performing preliminary alignment .. "
- if entiresearch == 1 then
--# system( mafftpath + " --maxiterate 1000 --localpair /tmp/_if#{$$} > /tmp/_pf#{$$}" )
-- system( mafftpath + " --maxiterate 0 --retree 2 /tmp/_if#{$$} > /tmp/_pf#{$$}" )
-+# system( mafftpath + " --maxiterate 1000 --localpair #{temp_if} > #{temp_pf}" )
-+ system( mafftpath + " --maxiterate 0 --retree 2 #{temp_if} > #{temp_pf}" )
- else
-- system( mafftpath + " --maxiterate 1000 --localpair --core --coreext --corethr #{corethr.to_s} --corewin #{corewin.to_s} /tmp/_if#{$$} > /tmp/_pf#{$$}" )
-+ system( mafftpath + " --maxiterate 1000 --localpair --core --coreext --corethr #{corethr.to_s} --corewin #{corewin.to_s} #{temp_if} > #{temp_pf}" )
- end
- end
-
--pfp = File.open( "/tmp/_pf#{$$}", 'r' )
-+pfp = File.open( "#{temp_pf}", 'r' )
- inname = []
- inseq = []
- slen = []
-@@ -155,7 +169,7 @@
- end
- pfp.close
-
--pfp = File.open( "/tmp/_if#{$$}", 'r' )
-+pfp = File.open( "#{temp_if}", 'r' )
- orname = []
- orseq = []
- nin = 0
-@@ -188,7 +202,7 @@
- #p act
-
-
--afp = File.open( "/tmp/_af#{$$}", 'w' )
-+afp = File.open( "#{temp_af}", 'w' )
-
- STDERR.puts "Searching .. \n"
- ids = []
-@@ -209,10 +223,10 @@
- end
-
- if local == 0 then
-- command = "lynx -source 'http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?QUERY=" + inseq[i] + "&DATABASE=swissprot&HITLIST_SIZE=" + nadd.to_s + "&FILTER=L&EXPECT='" + eval.to_s + "'&FORMAT_TYPE=TEXT&PROGRAM=blastp&SERVICE=plain&NCBI_GI=on&PAGE=Proteins&CMD=Put' > /tmp/_rid#{$$}"
-+ command = "lynx -source 'http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?QUERY=" + inseq[i] + "&DATABASE=swissprot&HITLIST_SIZE=" + nadd.to_s + "&FILTER=L&EXPECT='" + eval.to_s + "'&FORMAT_TYPE=TEXT&PROGRAM=blastp&SERVICE=plain&NCBI_GI=on&PAGE=Proteins&CMD=Put' > #{temp_rid}"
- system command
-
-- ridp = File.open( "/tmp/_rid#{$$}", 'r' )
-+ ridp = File.open( "#{temp_rid}", 'r' )
- while ridp.gets
- break if $_ =~ / RID = (.*)/
- end
-@@ -224,9 +238,9 @@
- while 1
- STDERR.printf "."
- sleep 10
-- command = "lynx -source 'http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?RID=" + rid + "&DESCRIPTIONS=500&ALIGNMENTS=" + nadd.to_s + "&ALIGNMENT_TYPE=Pairwise&OVERVIEW=no&CMD=Get&FORMAT_TYPE=XML' > /tmp/_res#{$$}"
-+ command = "lynx -source 'http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?RID=" + rid + "&DESCRIPTIONS=500&ALIGNMENTS=" + nadd.to_s + "&ALIGNMENT_TYPE=Pairwise&OVERVIEW=no&CMD=Get&FORMAT_TYPE=XML' > #{temp_res}"
- system command
-- resp = File.open( "/tmp/_res#{$$}", 'r' )
-+ resp = File.open( "#{temp_res}", 'r' )
- # resp.gets
- # if $_ =~ /WAITING/ then
- # resp.close
-@@ -247,17 +261,17 @@
- else
- # puts "Not supported"
- # exit
-- qfp = File.open( "/tmp/_q#{$$}", 'w' )
-+ qfp = File.open( "#{temp_qf}", 'w' )
- qfp.puts "> "
- qfp.puts inseq[i]
- qfp.close
-- command = blastpath + " -p blastp -e #{eval} -b 1000 -m 7 -i /tmp/_q#{$$} -d #{localdb} > /tmp/_res#{$$}"
-+ command = blastpath + " -p blastp -e #{eval} -b 1000 -m 7 -i #{temp_qf} -d #{localdb} > #{temp_res}"
- system command
-- resp = File.open( "/tmp/_res#{$$}", 'r' )
-+ resp = File.open( "#{temp_res}", 'r' )
- end
- STDERR.puts " Done.\n\n"
-
-- resp = File.open( "/tmp/_res#{$$}", 'r' )
-+ resp = File.open( "#{temp_res}", 'r' )
- while 1
- while resp.gets
- break if $_ =~ /<Hit_id>(.*)<\/Hit_id>/ || $_ =~ /(<Iteration_stat>)/
-@@ -310,17 +324,15 @@
- afp.close
-
- STDERR.puts "Performing alignment .. "
--system( mafftpath + mafftopt + " /tmp/_af#{$$} > /tmp/_bf#{$$}" )
-+system( mafftpath + mafftopt + " #{temp_af} > #{temp_bf}" )
- STDERR.puts "done."
-
--bfp = File.open( "/tmp/_bf#{$$}", 'r' )
-+bfp = File.open( "#{temp_bf}", 'r' )
- outseq = []
- outnam = []
- readfasta( bfp, outnam, outseq )
- bfp.close
-
--
--
- outseq2 = []
- outnam2 = []
-
-@@ -356,5 +368,3 @@
- puts ">" + outnam2[i]
- puts outseq2[i].gsub( /.{1,60}/, "\\0\n" )
- end
--
--system( "rm -rf /tmp/_if#{$$} /tmp/_vf#{$$} /tmp/_af#{$$} /tmp/_bf#{$$} /tmp/_pf#{$$} /tmp/_q#{$$} /tmp/_res#{$$} /tmp/_rid#{$$}" )
-diff -Naur mafft-6.240/src/mafft.tmpl mafft-6.240.new/src/mafft.tmpl
---- mafft-6.240/src/mafft.tmpl 2007-04-03 19:16:51.000000000 -0400
-+++ mafft-6.240.new/src/mafft.tmpl 2008-09-05 17:18:04.000000000 -0400
-@@ -240,11 +240,14 @@
- shift
- done;
-
--# TMPFILE=/tmp/`basename $0`.`whoami`.$$.`date +%y%m%d%H%M%S`
-- TMPFILE=/tmp/$progname.$$
-+ # create temporary directory; terminate script in case of failure
-+ if ! TMPFILE=`mktemp -dt $progname.XXXXXXXXXX`; then
-+ echo "Failed to create temporary directory"
-+ exit 1
-+ fi
-+
- umask 077
-- mkdir $TMPFILE || er=1
-- trap "rm -r $TMPFILE " 0
-+ trap "rm -rf $TMPFILE " 0
- if [ $# -eq 1 ]; then
- if [ -r "$1" -o "$1" = - ]; then
- cat "$1" | tr "\r" "\n" > $TMPFILE/infile
--- /dev/null
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/mafft/mafft-7.215.ebuild,v 1.1 2015/03/29 14:48:58 jlec Exp $
+
+EAPI=5
+
+inherit eutils flag-o-matic multilib toolchain-funcs
+
+EXTENSIONS="-without-extensions"
+
+DESCRIPTION="Multiple sequence alignments using a variety of algorithms"
+HOMEPAGE="http://mafft.cbrc.jp/alignment/software/index.html"
+SRC_URI="http://mafft.cbrc.jp/alignment/software/${P}${EXTENSIONS}-src.tgz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
+IUSE="threads"
+
+S="${WORKDIR}"/${P}${EXTENSIONS}
+
+src_prepare() {
+# epatch "${FILESDIR}"/${PN}-7.037-respect.patch
+ use threads && append-cppflags -Denablemultithread
+# sed "s:GENTOOLIBDIR:$(get_libdir):g" -i core/Makefile || die
+ sed -i -e "s/(PREFIX)\/man/(PREFIX)\/share\/man/" "${S}"/core/Makefile || die "sed failed"
+ sed \
+ -e 's:$(LDFLAGS)::g' \
+ -e 's:$(CC) -o $@:$(CC) $(LDFLAGS) -o $@:g' \
+ -e 's:$(CC) -shared -o $@:$(CC) $(LDFLAGS) -shared -o $@:g' \
+ -e '/INSTALL/s: -s : :g' \
+ -i core/Makefile || die
+}
+
+src_compile() {
+ cd core || die
+ emake \
+ $(usex threads ENABLE_MULTITHREAD="-Denablemultithread" ENABLE_MULTITHREAD="") \
+ PREFIX="${EPREFIX}"/usr \
+ CC="$(tc-getCC)" \
+ CFLAGS="${CFLAGS} -Wno-unused-result"
+}
+
+src_test() {
+ export MAFFT_BINARIES="${S}"/core
+ cd test || die
+ bash ../core/mafft sample > test.fftns2 || die
+ bash ../core/mafft --maxiterate 100 sample > test.fftnsi || die
+ bash ../core/mafft --globalpair sample > test.gins1 || die
+ bash ../core/mafft --globalpair --maxiterate 100 sample > test.ginsi || die
+ bash ../core/mafft --localpair sample > test.lins1 || die
+ bash ../core/mafft --localpair --maxiterate 100 sample > test.linsi || die
+
+ diff test.fftns2 sample.fftns2 || die
+ diff test.fftnsi sample.fftnsi || die
+ diff test.gins1 sample.gins1 || die
+ diff test.ginsi sample.ginsi || die
+ diff test.lins1 sample.lins1 || die
+}
+
+src_install() {
+ dodoc readme
+ cd core || die
+ emake PREFIX="${ED}usr" install
+}
projects / gentoo.git / commitdiff