* [gentoo-commits] proj/sci:master commit in: sci-biology/cegma/
@ 2015-01-10 1:21 Martin Mokrejs
0 siblings, 0 replies; 3+ messages in thread
From: Martin Mokrejs @ 2015-01-10 1:21 UTC (permalink / raw
To: gentoo-commits
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>
^ permalink raw reply related [flat|nested] 3+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/cegma/
@ 2015-01-10 14:07 Justin Lecher
0 siblings, 0 replies; 3+ messages in thread
From: Justin Lecher @ 2015-01-10 14:07 UTC (permalink / raw
To: gentoo-commits
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
^ permalink raw reply related [flat|nested] 3+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/cegma/
@ 2015-04-17 21:59 Martin Mokrejs
0 siblings, 0 replies; 3+ messages in thread
From: Martin Mokrejs @ 2015-04-17 21:59 UTC (permalink / raw
To: gentoo-commits
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."
}
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