commit: 6af4aac14e752bcd1bb065b0e09ded7c58ad088a Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Sat May 2 13:02:50 2015 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Sat May 2 13:02:50 2015 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=6af4aac1
sci-biology/twinscan: lots of tweaks to install process, install perl modules, more perl scripts, noted optional external dependencies Package-Manager: portage-2.2.18 sci-biology/twinscan/ChangeLog | 10 ++++- sci-biology/twinscan/twinscan-4.1.2-r1.ebuild | 62 +++++++++++++++++++++++++++ sci-biology/twinscan/twinscan-4.1.2.ebuild | 49 --------------------- 3 files changed, 70 insertions(+), 51 deletions(-) diff --git a/sci-biology/twinscan/ChangeLog b/sci-biology/twinscan/ChangeLog index fedf86e..a377384 100644 --- a/sci-biology/twinscan/ChangeLog +++ b/sci-biology/twinscan/ChangeLog @@ -1,7 +1,14 @@ # ChangeLog for sci-biology/twinscan -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*twinscan-4.1.2-r1 (02 May 2015) + + 02 May 2015; Martin Mokrejs <mmokr...@fold.natur.cuni.cz> + +twinscan-4.1.2-r1.ebuild, -twinscan-4.1.2.ebuild: + sci-biology/twinscan: lots of tweaks to install process, install perl modules, + more perl scripts, noted optional external dependencies + 16 Jun 2013; Justin Lecher <j...@gentoo.org> twinscan-4.1.2.ebuild, metadata.xml: Bump to EAPI=5 and fix license @@ -15,4 +22,3 @@ 17 Apr 2009; Andrey Kislyuk <wea...@gentoo.org> ChangeLog: New package, bug 154939, ebuild written by me - diff --git a/sci-biology/twinscan/twinscan-4.1.2-r1.ebuild b/sci-biology/twinscan/twinscan-4.1.2-r1.ebuild new file mode 100644 index 0000000..11500ca --- /dev/null +++ b/sci-biology/twinscan/twinscan-4.1.2-r1.ebuild @@ -0,0 +1,62 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +PERL_EXPORT_PHASE_FUNCTIONS=no +inherit perl-module eutils toolchain-funcs + +DESCRIPTION="iscan (aka twinscan and N-SCAN) and wrapper around Pairagon: A gene structure prediction pipeline" +HOMEPAGE="http://mblab.wustl.edu/software/twinscan"; +SRC_URI="http://mblab.wustl.edu/software/download/iscan-${PV}.tar_.gz -> ${P}.tar.gz" + +LICENSE="all-rights-reserved" +SLOT="0" +IUSE="" +KEYWORDS="~amd64 ~x86" + +DEPEND="dev-libs/glib:2" +RDEPEND="${DEPEND}" + +S="${WORKDIR}/N-SCAN" + +src_prepare() { + sed "1 a use lib '/usr/share/${PN}/lib/perl5';" -i "${S}"/bin/*.pl || die + sed '/my $blast_param/ s/#//' -i "${S}/bin/runTwinscan2.pl" || die + tc-export CC AR RANLIB + + sed \ + -e 's:ar :$(AR) :g' \ + -e 's:ranlib :$(RANLIB) :g' \ + -e 's: -o : $(LDFLAGS) -o :g' \ + -i Makefile || die + + sed \ + -e "/^GLIB_CFLAGS/s:=.*:=$($(tc-getPKG_CONFIG) --cflags glib-2.0) -DHAS_GLIB:g" \ + -e "/^GLIB_LFLAGS/s:=.*:=$($(tc-getPKG_CONFIG) --libs glib-2.0)-DHAS_GLIB:g" \ + -i Makefile.include || die +} + +src_install() { + dobin bin/iscan bin/zoe2gtf bin/*.pl src/*.pl + dolib lib/libzoe.a + insinto /usr/share/${PN} + doins -r parameters + insinto /usr/share/${PN}/src + doins src/*.zhmm + perl_set_version + insinto ${VENDOR_LIB}/${PN} + doins lib/perl5/*.pm + echo "TWINSCAN=/usr" > "${S}"/99${PN} + doenvd "${S}"/99${PN} + rm -rf examples/tmp + dodoc examples/* README* src/doc/*.txt +} + +pkg_postinst(){ + einfo "Pairagon acts on output from either: sci-biology/gmap sci-biology/blat." + einfo "It also works on blastn output from WU-BLAST (not provided in Gentoo)." + einfo "It also calls blastz (seems superseded by LASTZ) and genscan++ (not provided in Gentoo)." + einfo "For some reason we have pslCDnaFilter provided only by sci-biology/ucsc-genome-browser" +} diff --git a/sci-biology/twinscan/twinscan-4.1.2.ebuild b/sci-biology/twinscan/twinscan-4.1.2.ebuild deleted file mode 100644 index 4667c0e..0000000 --- a/sci-biology/twinscan/twinscan-4.1.2.ebuild +++ /dev/null @@ -1,49 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -inherit toolchain-funcs - -DESCRIPTION="TwinScan, N-SCAN, and Pairagon: A gene structure prediction pipeline" -HOMEPAGE="http://mblab.wustl.edu/software/twinscan"; -SRC_URI="http://mblab.wustl.edu/software/download/iscan-${PV}.tar_.gz -> ${P}.tar.gz" - -LICENSE="all-rights-reserved" -SLOT="0" -IUSE="" -KEYWORDS="~amd64 ~x86" - -DEPEND="dev-libs/glib:2" -RDEPEND="${DEPEND}" - -S="${WORKDIR}/N-SCAN" - -src_prepare() { - sed -i "1 a use lib '/usr/share/${PN}/lib/perl5';" "${S}"/bin/*.pl || die - sed -i '/my $blast_param/ s/#//' "${S}/bin/runTwinscan2.pl" || die - tc-export CC AR RANLIB - - sed \ - -e 's:ar :$(AR) :g' \ - -e 's:ranlib :$(RANLIB) :g' \ - -e 's: -o : $(LDFLAGS) -o :g' \ - -i Makefile || die - - sed \ - -e "/^GLIB_CFLAGS/s:=.*:=$($(tc-getPKG_CONFIG) --cflags glib-2.0) -DHAS_GLIB:g" \ - -e "/^GLIB_LFLAGS/s:=.*:=$($(tc-getPKG_CONFIG) --libs glib-2.0)-DHAS_GLIB:g" \ - -i Makefile.include || die -} - -src_install() { - dobin "${S}/bin/iscan" "${S}"/bin/*.pl || die - insinto /usr/share/${PN} - doins -r "${S}/parameters" || die - doins -r "${S}/lib" || die - echo "TWINSCAN=/usr" > "${S}"/99${PN} - doenvd "${S}"/99${PN} || die - rm -rf examples/tmp - dodoc examples/* README* -}
