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

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

[Martin Mokrejs]

commit:     7b043728312fa444242a9713c43332cd0bea44b5
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Mar  9 17:11:20 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Mar  9 17:11:20 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=7b043728

new package, working ebuild

Package-Manager: portage-2.2.15

 sci-biology/ORFcor/ChangeLog              |  9 +++++++++
 sci-biology/ORFcor/ORFcor-20130507.ebuild | 27 +++++++++++++++++++++++++++
 sci-biology/ORFcor/metadata.xml           |  9 +++++++++
 3 files changed, 45 insertions(+)

diff --git a/sci-biology/ORFcor/ChangeLog b/sci-biology/ORFcor/ChangeLog
new file mode 100644
index 0000000..7119777
--- /dev/null
+++ b/sci-biology/ORFcor/ChangeLog
@@ -0,0 +1,9 @@
+# ChangeLog for sci-biology/ORFcor
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*ORFcor-20130507 (09 Mar 2015)
+
+  09 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  +ORFcor-20130507.ebuild, +metadata.xml:
+  new package, working ebuild

diff --git a/sci-biology/ORFcor/ORFcor-20130507.ebuild b/sci-biology/ORFcor/ORFcor-20130507.ebuild
new file mode 100644
index 0000000..ad9c638
--- /dev/null
+++ b/sci-biology/ORFcor/ORFcor-20130507.ebuild
@@ -0,0 +1,27 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+DESCRIPTION="Automated editor of protein-coding sequences"
+HOMEPAGE="http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0058387"
+SRC_URI="http://www.currielab.wisc.edu/files/ORFcor.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+DEPEND="dev-lang/perl
+	sci-biology/hmmer
+	sci-biology/muscle
+	dev-perl/Parallel-ForkManager"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"/ORFcor
+
+src_install(){
+	dobin *.pl
+	dodoc README
+}

diff --git a/sci-biology/ORFcor/metadata.xml b/sci-biology/ORFcor/metadata.xml
new file mode 100644
index 0000000..2bc8930
--- /dev/null
+++ b/sci-biology/ORFcor/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>

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

[Martin Mokrejs]

commit:     1f9f01bf43c806a85a6df72031d4c1dd1d5fdad4
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Apr 17 22:56:25 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Apr 17 22:56:25 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=1f9f01bf

sci-biology/ORFcor: more cleanup

Package-Manager: portage-2.2.18

 sci-biology/ORFcor/ChangeLog              | 4 ++++
 sci-biology/ORFcor/ORFcor-20130507.ebuild | 6 +++++-
 2 files changed, 9 insertions(+), 1 deletion(-)

diff --git a/sci-biology/ORFcor/ChangeLog b/sci-biology/ORFcor/ChangeLog
index 7119777..86b3882 100644
--- a/sci-biology/ORFcor/ChangeLog
+++ b/sci-biology/ORFcor/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  17 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  ORFcor-20130507.ebuild:
+  sci-biology/ORFcor: more cleanup
+
 *ORFcor-20130507 (09 Mar 2015)
 
   09 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>

diff --git a/sci-biology/ORFcor/ORFcor-20130507.ebuild b/sci-biology/ORFcor/ORFcor-20130507.ebuild
index ad9c638..f338df0 100644
--- a/sci-biology/ORFcor/ORFcor-20130507.ebuild
+++ b/sci-biology/ORFcor/ORFcor-20130507.ebuild
@@ -14,9 +14,9 @@ KEYWORDS="~amd64"
 IUSE=""
 
 DEPEND="dev-lang/perl
-	sci-biology/hmmer
 	sci-biology/muscle
 	dev-perl/Parallel-ForkManager"
+	# >=sci-biology/hmmer-3.0
 RDEPEND="${DEPEND}"
 
 S="${WORKDIR}"/ORFcor
@@ -24,4 +24,8 @@ S="${WORKDIR}"/ORFcor
 src_install(){
 	dobin *.pl
 	dodoc README
+	insinto /usr/share/${PN}
+	doins 31_HMM*
+	insinto /usr/share/${PN}/test_data
+	doins test_data/*
 }