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

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

[Justin Lecher]

commit:     62133b81b8699efdb44997526481b4ec2ae87ad7
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Jan 10 14:10:28 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Jan 10 14:10:28 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=62133b81

sci-biology/cegma: Fix license;drop keywords due to missing keyowrds of deps

Package-Manager: portage-2.2.15

---
 sci-biology/cegma/ChangeLog        | 3 +++
 sci-biology/cegma/cegma-2.5.ebuild | 9 +++++----
 2 files changed, 8 insertions(+), 4 deletions(-)

diff --git a/sci-biology/cegma/ChangeLog b/sci-biology/cegma/ChangeLog
index 8e87015..aae6086 100644
--- a/sci-biology/cegma/ChangeLog
+++ b/sci-biology/cegma/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  10 Jan 2015; Justin Lecher <jlec@gentoo.org> cegma-2.5.ebuild:
+  Fix license;drop keywords due to missing keyowrds of deps
+
   10 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +cegma-2.5.ebuild,
   +metadata.xml:
   new package; install *.pm into PERL5LIB/cegma and pass that via env.d

diff --git a/sci-biology/cegma/cegma-2.5.ebuild b/sci-biology/cegma/cegma-2.5.ebuild
index ef8dfe5..bbc1199 100644
--- a/sci-biology/cegma/cegma-2.5.ebuild
+++ b/sci-biology/cegma/cegma-2.5.ebuild
@@ -4,16 +4,17 @@
 
 EAPI=5
 
-DESCRIPTION="Use set of 458 core proteins to predict genes in a genome and use them for training to find all genes"
+DESCRIPTION="Predict genes in a genome and use them for training to find all genes"
 HOMEPAGE="http://korflab.ucdavis.edu/datasets/cegma"
-SRC_URI="http://korflab.ucdavis.edu/datasets/cegma/CEGMA_v"${PV}".tar.gz"
+SRC_URI="http://korflab.ucdavis.edu/datasets/cegma/CEGMA_v${PV}.tar.gz"
 
 LICENSE="GPL-2"
 SLOT="0"
-KEYWORDS="~amd64"
+KEYWORDS=""
 IUSE=""
 
-DEPEND="dev-lang/perl
+DEPEND="
+	dev-lang/perl
 	sci-biology/wise
 	>=sci-biology/hmmer-3.0
 	sci-biology/geneid

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

[Martin Mokrejs]

commit:     be568843cdf33c76d056f5cd84d221bd57b78dbc
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Apr 17 21:36:50 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Apr 17 21:36:50 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=be568843

sci-biology/cegma: re-added KEYWORDS because sci-biology/ncbi-tools++ is now available; fixed installation of perl-related files; dropped hmmer from DEPEND

Package-Manager: portage-2.2.18

 sci-biology/cegma/ChangeLog        |  5 ++++-
 sci-biology/cegma/cegma-2.5.ebuild | 22 ++++++++++++----------
 2 files changed, 16 insertions(+), 11 deletions(-)

diff --git a/sci-biology/cegma/ChangeLog b/sci-biology/cegma/ChangeLog
index aae6086..760074c 100644
--- a/sci-biology/cegma/ChangeLog
+++ b/sci-biology/cegma/ChangeLog
@@ -2,10 +2,13 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  17 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> cegma-2.5.ebuild:
+  sci-biology/cegma: re-added KEYWORDS because sci-biology/ncbi-tools++ is now
+  available; fixed installation of perl-related files; dropped hmmer from DEPEND
+
   10 Jan 2015; Justin Lecher <jlec@gentoo.org> cegma-2.5.ebuild:
   Fix license;drop keywords due to missing keyowrds of deps
 
   10 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +cegma-2.5.ebuild,
   +metadata.xml:
   new package; install *.pm into PERL5LIB/cegma and pass that via env.d
-

diff --git a/sci-biology/cegma/cegma-2.5.ebuild b/sci-biology/cegma/cegma-2.5.ebuild
index bbc1199..ba9f799 100644
--- a/sci-biology/cegma/cegma-2.5.ebuild
+++ b/sci-biology/cegma/cegma-2.5.ebuild
@@ -4,34 +4,36 @@
 
 EAPI=5
 
+PERL_EXPORT_PHASE_FUNCTIONS=no
+inherit perl-module eutils toolchain-funcs
+
 DESCRIPTION="Predict genes in a genome and use them for training to find all genes"
 HOMEPAGE="http://korflab.ucdavis.edu/datasets/cegma"
 SRC_URI="http://korflab.ucdavis.edu/datasets/cegma/CEGMA_v${PV}.tar.gz"
 
 LICENSE="GPL-2"
 SLOT="0"
-KEYWORDS=""
+KEYWORDS="~amd64"
 IUSE=""
 
 DEPEND="
-	dev-lang/perl
 	sci-biology/wise
-	>=sci-biology/hmmer-3.0
 	sci-biology/geneid
 	sci-biology/ncbi-tools++"
+	# >=sci-biology/hmmer-3.0
 RDEPEND="${DEPEND}"
 
 S="${WORKDIR}"/CEGMA_v${PV}
 
 src_install(){
 	dobin bin/*
-	eval `perl '-V:installvendorlib'`
-	vendor_lib_install_dir="${installvendorlib}"
-	dodir ${vendor_lib_install_dir}/cegma
-	insinto ${vendor_lib_install_dir}/cegma
+	perl_set_version
+	insinto ${VENDOR_LIB}
 	doins lib/*.pm
+}
 
-	echo "PERL5LIB="${vendor_lib_install_dir}"/cegma" > ${S}"/99cegma"
-	# echo "CEGMATMP=/var/tmp" >> ${S}"/99cegma"
-	doenvd ${S}"/99cegma" || die
+pkg_postinst(){
+	ewarn "cegma needs >=sci-biology/hmmer-3.0 but sci-biology/wise uses sci-biology/hmmer-2.3"
+	ewarn "hmmer-3 is not backwards compatible and does not even have all its previous features"
+	ewarn "Therefore, we do not list hmmer in the list of DEPENDENCIES."
 }

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

[Martin Mokrejs]

commit:     f1305f2410140aee98085c7448eae116695a4b04
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat Jan 10 01:20:02 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat Jan 10 01:20:02 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=f1305f24

new package; install *.pm into PERL5LIB/cegma and pass that via env.d

---
 sci-biology/cegma/ChangeLog        |  8 ++++++++
 sci-biology/cegma/cegma-2.5.ebuild | 36 ++++++++++++++++++++++++++++++++++++
 sci-biology/cegma/metadata.xml     |  9 +++++++++
 3 files changed, 53 insertions(+)

diff --git a/sci-biology/cegma/ChangeLog b/sci-biology/cegma/ChangeLog
new file mode 100644
index 0000000..8e87015
--- /dev/null
+++ b/sci-biology/cegma/ChangeLog
@@ -0,0 +1,8 @@
+# ChangeLog for sci-biology/cegma
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+  10 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +cegma-2.5.ebuild,
+  +metadata.xml:
+  new package; install *.pm into PERL5LIB/cegma and pass that via env.d
+

diff --git a/sci-biology/cegma/cegma-2.5.ebuild b/sci-biology/cegma/cegma-2.5.ebuild
new file mode 100644
index 0000000..ef8dfe5
--- /dev/null
+++ b/sci-biology/cegma/cegma-2.5.ebuild
@@ -0,0 +1,36 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+DESCRIPTION="Use set of 458 core proteins to predict genes in a genome and use them for training to find all genes"
+HOMEPAGE="http://korflab.ucdavis.edu/datasets/cegma"
+SRC_URI="http://korflab.ucdavis.edu/datasets/cegma/CEGMA_v"${PV}".tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+DEPEND="dev-lang/perl
+	sci-biology/wise
+	>=sci-biology/hmmer-3.0
+	sci-biology/geneid
+	sci-biology/ncbi-tools++"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"/CEGMA_v${PV}
+
+src_install(){
+	dobin bin/*
+	eval `perl '-V:installvendorlib'`
+	vendor_lib_install_dir="${installvendorlib}"
+	dodir ${vendor_lib_install_dir}/cegma
+	insinto ${vendor_lib_install_dir}/cegma
+	doins lib/*.pm
+
+	echo "PERL5LIB="${vendor_lib_install_dir}"/cegma" > ${S}"/99cegma"
+	# echo "CEGMATMP=/var/tmp" >> ${S}"/99cegma"
+	doenvd ${S}"/99cegma" || die
+}

diff --git a/sci-biology/cegma/metadata.xml b/sci-biology/cegma/metadata.xml
new file mode 100644
index 0000000..2bc8930
--- /dev/null
+++ b/sci-biology/cegma/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci-biology</herd>
+  <maintainer>
+    <email>mmokrejs@fold.natur.cuni.cz</email>
+    <name>Martin Mokrejs</name>
+  </maintainer>
+</pkgmetadata>