commit: 11549cfb4998ee1344504f07e933eb2e224de5f8 Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net> AuthorDate: Mon Jan 18 12:59:57 2021 +0000 Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net> CommitDate: Mon Jan 18 12:59:57 2021 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=11549cfb
sci-biology/twinscan: remove pack, obsolete and replaced upstream Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net> profiles/package.mask | 1 - sci-biology/twinscan/metadata.xml | 8 ---- sci-biology/twinscan/twinscan-4.1.2-r1.ebuild | 64 --------------------------- 3 files changed, 73 deletions(-) diff --git a/profiles/package.mask b/profiles/package.mask index 4addb8cbf..04a82cd44 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -113,4 +113,3 @@ sci-biology/swissknife sci-biology/tablet-bin sci-biology/TransDecoder sci-biology/trim_galore -sci-biology/twinscan diff --git a/sci-biology/twinscan/metadata.xml b/sci-biology/twinscan/metadata.xml deleted file mode 100644 index 8417d1580..000000000 --- a/sci-biology/twinscan/metadata.xml +++ /dev/null @@ -1,8 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> -<pkgmetadata> - <maintainer type="project"> - <email>[email protected]</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-biology/twinscan/twinscan-4.1.2-r1.ebuild b/sci-biology/twinscan/twinscan-4.1.2-r1.ebuild deleted file mode 100644 index 7c8993f9f..000000000 --- a/sci-biology/twinscan/twinscan-4.1.2-r1.ebuild +++ /dev/null @@ -1,64 +0,0 @@ -# Copyright 1999-2016 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -PERL_EXPORT_PHASE_FUNCTIONS=no -inherit perl-module eutils toolchain-funcs - -DESCRIPTION="iscan (aka twinscan and N-SCAN), Pairagon wrapper: Gene structure pred. 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 : $(LDFLAGS) -o :g' \ - -i Makefile || die - - sed \ - -e "/^GLIB_CFLAGS/s:=.*:=$($(tc-getPKG_CONFIG) --cflags glib-2.0) -DHAS_GLIB:g" \ - -e "/^GLIB_LFLAGS/s:=.*:=$($(tc-getPKG_CONFIG) --libs glib-2.0) -DHAS_GLIB:g" \ - -i Makefile.include || die -} - -src_install() { - # TODO: prevent file collision with media-gfx/iscan by renaming iscan to iscan_twinscan - # also fix a Genscan++ToZoe.pl Nscan_driver.pl runTwinscan2.pl run_iscan.pl run_iscan_cons.pl run_iscan_cons_list.pl test.pl - rm src/test.pl || die - dobin bin/iscan bin/zoe2gtf bin/*.pl src/*.pl - dolib lib/libzoe.a - insinto /usr/share/${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" -}
