Version BUmp; drop obsolete patch

(Portage version: 2.2.18/cvs/Linux x86_64, signed Manifest commit with key B9D4F231BD1558AB!)

3 files changed, 73 insertions, 194 deletions

diff --git a/sci-biology/mafft/ChangeLog b/sci-biology/mafft/ChangeLog
index 4e1232d70c53..57482dbec986 100644
--- a/sci-biology/mafft/ChangeLog
+++ b/sci-biology/mafft/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/mafft
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/mafft/ChangeLog,v 1.20 2013/07/19 09:44:31 jlec Exp $
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/mafft/ChangeLog,v 1.21 2015/03/29 14:48:58 jlec Exp $
+
+*mafft-7.215 (29 Mar 2015)
+
+  29 Mar 2015; Justin Lecher <jlec@gentoo.org> +mafft-7.215.ebuild,
+  -files/mafft-6.240-mktemp.patch:
+  Version BUmp; drop obsolete patch
 
   19 Jul 2013; Justin Lecher <jlec@gentoo.org> mafft-7.050.ebuild:
   Keyword for ~-linux
@@ -103,4 +109,3 @@
   21 Oct 2006; Donnie Berkholz <dberkholz@gentoo.org>; +metadata.xml,
   +mafft-5.861.ebuild:
   New package: Multiple sequence alignments using a variety of algorithms.
-
diff --git a/sci-biology/mafft/files/mafft-6.240-mktemp.patch b/sci-biology/mafft/files/mafft-6.240-mktemp.patch
deleted file mode 100644
index 1b96c8f47204..000000000000
--- a/sci-biology/mafft/files/mafft-6.240-mktemp.patch
+++ /dev/null
@@ -1,191 +0,0 @@
-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 
diff --git a/sci-biology/mafft/mafft-7.215.ebuild b/sci-biology/mafft/mafft-7.215.ebuild
new file mode 100644
index 000000000000..9099751b828a
--- /dev/null
+++ b/sci-biology/mafft/mafft-7.215.ebuild
@@ -0,0 +1,65 @@
+# 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
+}