From: "Martin Mokrejs" <mmokrejs@fold.natur.cuni.cz>
To: gentoo-commits@lists.gentoo.org
Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/twinscan/
Date: Sat, 2 May 2015 13:03:32 +0000 (UTC) [thread overview]
Message-ID: <1430571770.6af4aac14e752bcd1bb065b0e09ded7c58ad088a.mmokrejs@gentoo> (raw)
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 <mmokrejs@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 <jlec@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 <weaver@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*
-}
next reply other threads:[~2015-05-02 13:03 UTC|newest]
Thread overview: 11+ messages / expand[flat|nested] mbox.gz Atom feed top
2015-05-02 13:03 Martin Mokrejs [this message]
-- strict thread matches above, loose matches on Subject: below --
2021-03-18 18:54 [gentoo-commits] proj/sci:master commit in: sci-biology/twinscan/ Andrew Ammerlaan
2021-03-06 16:45 Andrew Ammerlaan
2021-03-06 16:44 Andrew Ammerlaan
2021-03-06 16:43 Andrew Ammerlaan
2021-01-18 13:33 Andrew Ammerlaan
2021-01-18 13:13 Andrew Ammerlaan
2016-12-01 14:44 Martin Mokrejs
2016-08-01 11:18 Martin Mokrejs
2016-07-29 9:21 Martin Mokrejs
2011-03-07 12:01 Justin Lecher
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