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

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

[Martin Mokrejs]

commit:     2a8becfc2faa9ad23f8b0ee191fd7a2889156335
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Feb 16 18:03:35 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Feb 16 18:03:35 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=2a8becfc

sci-biology/cross_genome: new a package somewhat belonging to the phusion2 software bundle

Package-Manager: portage-2.2.26

 .../cross_genome/cross_genome-20140822.ebuild      | 29 ++++++++++++++++++++++
 sci-biology/cross_genome/metadata.xml              | 12 +++++++++
 2 files changed, 41 insertions(+)

diff --git a/sci-biology/cross_genome/cross_genome-20140822.ebuild b/sci-biology/cross_genome/cross_genome-20140822.ebuild
new file mode 100644
index 0000000..d85fec8
--- /dev/null
+++ b/sci-biology/cross_genome/cross_genome-20140822.ebuild
@@ -0,0 +1,29 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+DESCRIPTION="Genome scaffolding using cross-species synteny"
+HOMEPAGE="http://www.sanger.ac.uk/science/tools/crossgenome"
+SRC_URI="https://sourceforge.net/projects/phusion2/files/cross_genome/cross_genome.tar.gz -> cross_genome-20140822.tar.gz"
+
+LICENSE="GPL-3+"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"
+
+src_prepare(){
+	sed -e 's/^CC =/# CC =/' -i Makefile || die
+	sed -e 's/^CFLAGS =/# CFLAGS =/' -i Makefile || die
+}
+
+src_install(){
+	dobin cross_genome.csh cross_genome
+	dodoc README
+}

diff --git a/sci-biology/cross_genome/metadata.xml b/sci-biology/cross_genome/metadata.xml
new file mode 100644
index 0000000..1699e58
--- /dev/null
+++ b/sci-biology/cross_genome/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="person">
+    <email>mmokrejs@fold.natur.cuni.cz</email>
+    <name>Martin Mokrejs</name>
+  </maintainer>
+<maintainer type="project">
+    <email>sci-biology@gentoo.org</email>
+    <name>Gentoo Biology Project</name>
+  </maintainer>
+</pkgmetadata>

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

[Justin Lecher]

commit:     4f98cf388140dd5fb557129852ed06e4286df1cc
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Feb 17 14:06:33 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Feb 17 14:06:33 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=4f98cf38

sci-biology/cross_genome: Bump to EAPI=6

Package-Manager: portage-2.2.27
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 sci-biology/cross_genome/cross_genome-20140822.ebuild | 8 +++-----
 sci-biology/cross_genome/metadata.xml                 | 2 +-
 2 files changed, 4 insertions(+), 6 deletions(-)

diff --git a/sci-biology/cross_genome/cross_genome-20140822.ebuild b/sci-biology/cross_genome/cross_genome-20140822.ebuild
index d85fec8..259cc96 100644
--- a/sci-biology/cross_genome/cross_genome-20140822.ebuild
+++ b/sci-biology/cross_genome/cross_genome-20140822.ebuild
@@ -1,8 +1,8 @@
 # Copyright 1999-2016 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: $
+# $Id$
 
-EAPI=5
+EAPI=6
 
 DESCRIPTION="Genome scaffolding using cross-species synteny"
 HOMEPAGE="http://www.sanger.ac.uk/science/tools/crossgenome"
@@ -13,14 +13,12 @@ SLOT="0"
 KEYWORDS="~amd64"
 IUSE=""
 
-DEPEND=""
-RDEPEND="${DEPEND}"
-
 S="${WORKDIR}"
 
 src_prepare(){
 	sed -e 's/^CC =/# CC =/' -i Makefile || die
 	sed -e 's/^CFLAGS =/# CFLAGS =/' -i Makefile || die
+	default
 }
 
 src_install(){

diff --git a/sci-biology/cross_genome/metadata.xml b/sci-biology/cross_genome/metadata.xml
index 1699e58..f68a1b6 100644
--- a/sci-biology/cross_genome/metadata.xml
+++ b/sci-biology/cross_genome/metadata.xml
@@ -5,7 +5,7 @@
     <email>mmokrejs@fold.natur.cuni.cz</email>
     <name>Martin Mokrejs</name>
   </maintainer>
-<maintainer type="project">
+  <maintainer type="project">
     <email>sci-biology@gentoo.org</email>
     <name>Gentoo Biology Project</name>
   </maintainer>

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

[Martin Mokrejs]

commit:     f79c7da15fb569929a0c701f9bb0a95e695228a5
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Feb 17 22:53:05 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Feb 17 22:53:05 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=f79c7da1

sci-biology/cross_genome: donot install cross_genome.csh because it is not needed per info from upstream; upstream also states this pakcage does not need anything from the phusion2 bundle to be installed

Package-Manager: portage-2.2.26

 sci-biology/cross_genome/cross_genome-20140822.ebuild | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/sci-biology/cross_genome/cross_genome-20140822.ebuild b/sci-biology/cross_genome/cross_genome-20140822.ebuild
index 259cc96..1a29076 100644
--- a/sci-biology/cross_genome/cross_genome-20140822.ebuild
+++ b/sci-biology/cross_genome/cross_genome-20140822.ebuild
@@ -22,6 +22,7 @@ src_prepare(){
 }
 
 src_install(){
-	dobin cross_genome.csh cross_genome
+	# per upstream cross_genome.csh is not needed
+	dobin cross_genome
 	dodoc README
 }

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

[Martin Mokrejs]

commit:     0febc21229dd92abe0846f026d84959a734c9e00
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Mar 30 21:54:10 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Mar 30 21:54:10 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=0febc212

sci-biology/cross_genome: polish ebuild syntax

Package-Manager: portage-2.2.28

 sci-biology/cross_genome/cross_genome-20140822.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-biology/cross_genome/cross_genome-20140822.ebuild b/sci-biology/cross_genome/cross_genome-20140822.ebuild
index 1a29076..eca7e19 100644
--- a/sci-biology/cross_genome/cross_genome-20140822.ebuild
+++ b/sci-biology/cross_genome/cross_genome-20140822.ebuild
@@ -6,7 +6,7 @@ EAPI=6
 
 DESCRIPTION="Genome scaffolding using cross-species synteny"
 HOMEPAGE="http://www.sanger.ac.uk/science/tools/crossgenome"
-SRC_URI="https://sourceforge.net/projects/phusion2/files/cross_genome/cross_genome.tar.gz -> cross_genome-20140822.tar.gz"
+SRC_URI="https://sourceforge.net/projects/phusion2/files/cross_genome/cross_genome.tar.gz -> ${P}.tar.gz"
 
 LICENSE="GPL-3+"
 SLOT="0"