sci-biology/trnascan-se: Version BUmp, #532460

(Portage version: 2.2.15/cvs/Linux x86_64, signed Manifest commit with key B9D4F231BD1558AB!)

5 files changed, 91 insertions, 52 deletions

diff --git a/sci-biology/trnascan-se/ChangeLog b/sci-biology/trnascan-se/ChangeLog
index 3cb787b7d833..c8fc56f8b210 100644
--- a/sci-biology/trnascan-se/ChangeLog
+++ b/sci-biology/trnascan-se/ChangeLog
@@ -1,6 +1,13 @@
 # ChangeLog for sci-biology/trnascan-se
-# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/trnascan-se/ChangeLog,v 1.13 2010/07/16 22:09:08 hwoarang Exp $
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/trnascan-se/ChangeLog,v 1.14 2015/01/08 07:42:51 jlec Exp $
+
+*trnascan-se-1.31 (08 Jan 2015)
+
+  08 Jan 2015; Justin Lecher <jlec@gentoo.org> -trnascan-se-1.23-r1.ebuild,
+  +trnascan-se-1.31.ebuild, +files/trnascan-se-1.31-ldflags.patch,
+  metadata.xml:
+  Version BUmp, #532460
 
   16 Jul 2010; Markos Chandras <hwoarang@gentoo.org>
   trnascan-se-1.23-r2.ebuild:
diff --git a/sci-biology/trnascan-se/files/trnascan-se-1.31-ldflags.patch b/sci-biology/trnascan-se/files/trnascan-se-1.31-ldflags.patch
new file mode 100644
index 000000000000..f28b1e8f6bb0
--- /dev/null
+++ b/sci-biology/trnascan-se/files/trnascan-se-1.31-ldflags.patch
@@ -0,0 +1,26 @@
+diff --git a/Makefile b/Makefile
+index 53e5c5b..a2d3feb 100644
+--- a/Makefile
++++ b/Makefile
+@@ -109,17 +109,17 @@ MPOBJ = mpviterbi.o mp-dbviterbi.o
+ all: 	$(PROGS) tRNAscan-SE setpaths
+ 
+ covels-SE:  $(OBJ) scan_main.o
+-	$(CC) $(CFLAGS) $(RFLAGS) -o covels-SE scan_main.o $(OBJ) $(LIBS)
++	$(CC) $(CFLAGS) $(RFLAGS) $(LDFLAGS) -o covels-SE scan_main.o $(OBJ) $(LIBS)
+ 
+ coves-SE: $(OBJ) score_main.o
+-	$(CC) $(CFLAGS) $(RFLAGS) -o coves-SE score_main.o $(OBJ) $(LIBS)
++	$(CC) $(CFLAGS) $(RFLAGS) $(LDFLAGS) -o coves-SE score_main.o $(OBJ) $(LIBS)
+ 
+ eufindtRNA: $(SQUIDOBJ) pavesi.o eufind_main.o
+-	$(CC) $(CFLAGS)  -o eufindtRNA eufind_main.o \
++	$(CC) $(CFLAGS)  $(LDFLAGS) -o eufindtRNA eufind_main.o \
+ 	pavesi.o $(SQUIDOBJ) $(LIBS)
+ 
+ trnascan-1.4: trnascan.o
+-	$(CC) $(CFLAGS) -DTSCANDIR=\"$(LIBDIR)\" -o trnascan-1.4 trnascan.c
++	$(CC) $(CFLAGS) -DTSCANDIR=\"$(LIBDIR)\" $(LDFLAGS) -o trnascan-1.4 trnascan.c
+ 
+ tRNAscan-SE:
+ 	$(PERLDIR)/$(PERLBIN) checkversion.pl
diff --git a/sci-biology/trnascan-se/metadata.xml b/sci-biology/trnascan-se/metadata.xml
index 58c1938a82e7..55de1683677f 100644
--- a/sci-biology/trnascan-se/metadata.xml
+++ b/sci-biology/trnascan-se/metadata.xml
@@ -1,8 +1,8 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-	<herd>sci-biology</herd>
-	<longdescription>
+  <herd>sci-biology</herd>
+  <longdescription>
 		tRNAscan-SE detects ~99% of eukaryotic nuclear or prokaryotic tRNA
 		genes, with a false positive rate of less than one per 15 gigabases,
 		and with a search speed of about 30 kb/second. It was implemented for
diff --git a/sci-biology/trnascan-se/trnascan-se-1.23-r1.ebuild b/sci-biology/trnascan-se/trnascan-se-1.23-r1.ebuild
deleted file mode 100644
index b11d1e74d58b..000000000000
--- a/sci-biology/trnascan-se/trnascan-se-1.23-r1.ebuild
+++ /dev/null
@@ -1,48 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/trnascan-se/trnascan-se-1.23-r1.ebuild,v 1.6 2009/08/05 18:45:47 ssuominen Exp $
-
-inherit eutils toolchain-funcs
-
-DESCRIPTION="tRNA detection in large-scale genome sequences"
-HOMEPAGE="http://selab.wustl.edu/cgi-bin/selab.pl?mode=software#trnascan"
-SRC_URI="mirror://gentoo/${P}.tar.bz2"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 x86"
-IUSE=""
-
-RDEPEND="dev-lang/perl"
-DEPEND="${RDEPEND}"
-
-src_unpack() {
-	unpack ${A}
-	cd "${S}"
-	epatch "${FILESDIR}"/${P}-glibc-2.10.patch
-	sed -e "s%BINDIR  = \$(HOME)/bin%BINDIR = /usr/bin%" \
-		-e "s%LIBDIR  = \$(HOME)/lib/tRNAscan-SE%LIBDIR = /usr/lib/${PN}%" \
-		-e "s%MANDIR  = \$(HOME)/man%MANDIR = /usr/share/man%" \
-		-e "s%CC = gcc%CC = $(tc-getCC)%" \
-		-e "s%CFLAGS = -O%CFLAGS = ${CFLAGS}%" \
-		-i Makefile || die
-}
-
-src_compile() {
-	emake || die
-	mv tRNAscan-SE.man tRNAscan-SE.man.1 || die
-}
-
-src_install() {
-	dobin covels-SE coves-SE eufindtRNA tRNAscan-SE trnascan-1.4 || die
-	doman tRNAscan-SE.man.1 || die
-	dodoc MANUAL README Release.history || die
-	insinto /usr/lib/${PN}/
-	doins *.cm gcode.* Dsignal TPCsignal || die
-	insinto /usr/share/doc/${PF}
-	doins Manual.ps || die
-}
-
-src_test() {
-	make testrun || die
-}
diff --git a/sci-biology/trnascan-se/trnascan-se-1.31.ebuild b/sci-biology/trnascan-se/trnascan-se-1.31.ebuild
new file mode 100644
index 000000000000..bf80b106d04a
--- /dev/null
+++ b/sci-biology/trnascan-se/trnascan-se-1.31.ebuild
@@ -0,0 +1,54 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/trnascan-se/trnascan-se-1.31.ebuild,v 1.1 2015/01/08 07:42:51 jlec Exp $
+
+EAPI=5
+
+PERL_EXPORT_PHASE_FUNCTIONS=no
+
+inherit eutils perl-module toolchain-funcs
+
+DESCRIPTION="tRNA detection in large-scale genome sequences"
+HOMEPAGE="http://lowelab.ucsc.edu/tRNAscan-SE/"
+SRC_URI="http://lowelab.ucsc.edu/software/tRNAscan-SE.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+S="${WORKDIR}"/tRNAscan-SE-1.3.1/
+
+src_prepare() {
+	epatch \
+		"${FILESDIR}"/${P}-ldflags.patch
+	sed \
+		-e "s:BINDIR  = \$(HOME)/bin:BINDIR = ${EPREFIX}/usr/bin:" \
+		-e "s:LIBDIR  = \$(HOME)/lib/tRNAscan-SE:LIBDIR = ${EPRFIX}/usr/share/${PN}:" \
+		-e "s:MANDIR  = \$(HOME)/man:MANDIR = ${EPREFIX}/usr/share/man:" \
+		-e "s:CC = gcc:CC = $(tc-getCC):" \
+		-e "s:CFLAGS = -O:CFLAGS = ${CFLAGS}:" \
+		-i Makefile || die
+
+	perl_set_version
+}
+
+src_test() {
+	emake PATH="${S}:${PATH}" testrun
+}
+
+src_install() {
+	dobin covels-SE coves-SE eufindtRNA tRNAscan-SE trnascan-1.4
+
+	newman tRNAscan-SE.man tRNAscan-SE.man.1
+
+	dodoc MANUAL README Release.history
+
+	insinto /usr/share/${PN}/
+	doins *.cm gcode.* Dsignal TPCsignal
+
+	dodoc Manual.ps
+
+	insinto ${VENDOR_LIB}
+	doins -r tRNAscanSE
+}