From: Justin Lecher Date: Thu, 8 Jan 2015 07:42:52 +0000 (+0000) Subject: sci-biology/trnascan-se: Version BUmp, #532460 X-Git-Url: http://git.tremily.us/?a=commitdiff_plain;h=207fcef587561f9867f3cbe50897390323925470;p=gentoo.git sci-biology/trnascan-se: Version BUmp, #532460 Package-Manager: portage-2.2.15/cvs/Linux x86_64 Manifest-Sign-Key: 0xB9D4F231BD1558AB! --- 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 -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 trnascan-se-1.23-r2.ebuild: diff --git a/sci-biology/trnascan-se/Manifest b/sci-biology/trnascan-se/Manifest index 24d3ba6abc1c..9108667fc2bf 100644 --- a/sci-biology/trnascan-se/Manifest +++ b/sci-biology/trnascan-se/Manifest @@ -1,7 +1,31 @@ -AUX trnascan-se-1.23-glibc-2.10.patch 6702 RMD160 1ac6cf0d4630ae7c9f7cd55c209d3b7d7391b18e SHA1 a2a7017c37e8db122026a2066ae107428b05ac95 SHA256 16c6083f8a2991d22252a23184a45c74e0fd75b5a45085c3dcea7d1cd503cf42 -AUX trnascan-se-1.23-ldflags.patch 971 RMD160 93382a13c9b14e687a884fff06a926abd6ea634c SHA1 0561f26cea27f2ec6268b54383be6aeb07367c1f SHA256 6013162268bc78f6752ce8703d9fd1810f634a9176b55dac67155b8decb8e6e9 -DIST trnascan-se-1.23.tar.bz2 482202 RMD160 41180bc008e64258470a241418467b9b97220669 SHA1 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+ + 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 @@ - sci-biology - + sci-biology + 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 +}