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

[Martin Mokrejs]

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@×××××××××××××××.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@g.o> twinscan-4.1.2.ebuild,
   metadata.xml:
   Bump to EAPI=5 and fix license
@@ -15,4 +22,3 @@
 
   17 Apr 2009; Andrey Kislyuk <weaver@g.o> 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*
-}