[gentoo-commits] proj/sci:master commit in: sci-biology/twinscan/, profiles/

[gentoo-commits] proj/sci:master commit in: sci-biology/twinscan/, profiles/

[Andrew Ammerlaan]

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>sci-biology@gentoo.org</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"
-}