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

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

[Martin Mokrejs]

commit:     62afc0eb5df8a6b490373a37d801ff4e7d373613
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Feb 11 20:47:13 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Feb 11 20:47:13 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=62afc0eb

sci-biology/grass: new package, see bugs at github.com

Package-Manager: portage-2.2.26

 sci-biology/grass/grass-20130628.ebuild | 39 +++++++++++++++++++++++++++++++++
 sci-biology/grass/metadata.xml          | 12 ++++++++++
 2 files changed, 51 insertions(+)

diff --git a/sci-biology/grass/grass-20130628.ebuild b/sci-biology/grass/grass-20130628.ebuild
new file mode 100644
index 0000000..9744012
--- /dev/null
+++ b/sci-biology/grass/grass-20130628.ebuild
@@ -0,0 +1,39 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+DESCRIPTION="Scaffold next-generation sequencing assemblies"
+HOMEPAGE="https://github.com/AlexeyG/GRASS"
+SRC_URI="https://github.com/AlexeyG/GRASS/archive/master.zip -> grass-20130628.zip
+	https://tud-scaffolding.googlecode.com/files/GRASS%20manual.pdf -> grass_manual.pdf"
+# EGIT_REPO_URI="https://github.com/AlexeyG/GRASS.git"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+# some IBM development CPLEX library?
+# ilcplex/ilocplex.h: No such file or directory
+DEPEND="sci-biology/bamtools
+	sci-biology/ncbi-tools++"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"/GRASS-master
+
+src_prepare(){
+	sed -e 's#/data/bio/alexeygritsenk/apps/include/ncbi-tools++#/usr/include/ncbi-tools++#' -i Makefile.config || die
+	sed -e 's#/data/bio/alexeygritsenk/apps/include/#/usr/include/bamtools#' -i Makefile.config || die
+	sed -e 's#/data/bio/alexeygritsenk/apps/lib#/usr/lib64#' -i Makefile.config || die
+}
+
+src_compile(){
+	emake all
+}
+
+src_install(){
+	dodoc "${DISTDIR}"/grass_manual.pdf manual/manual.tex
+	dobin bin/*
+}

diff --git a/sci-biology/grass/metadata.xml b/sci-biology/grass/metadata.xml
new file mode 100644
index 0000000..1699e58
--- /dev/null
+++ b/sci-biology/grass/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/grass/

[Martin Mokrejs]

commit:     c726bb77b7342a410c7249d19739c82b5e8d5437
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Feb 11 21:11:48 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Feb 11 21:11:48 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=c726bb77

sci-biology/grass: add a link to https://github.com/AlexeyG/GRASS/issues/6

Package-Manager: portage-2.2.26

 sci-biology/grass/grass-20130628.ebuild | 1 +
 1 file changed, 1 insertion(+)

diff --git a/sci-biology/grass/grass-20130628.ebuild b/sci-biology/grass/grass-20130628.ebuild
index 9744012..d591da6 100644
--- a/sci-biology/grass/grass-20130628.ebuild
+++ b/sci-biology/grass/grass-20130628.ebuild
@@ -17,6 +17,7 @@ IUSE=""
 
 # some IBM development CPLEX library?
 # ilcplex/ilocplex.h: No such file or directory
+# https://github.com/AlexeyG/GRASS/issues/6
 DEPEND="sci-biology/bamtools
 	sci-biology/ncbi-tools++"
 RDEPEND="${DEPEND}"

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

[Martin Mokrejs]

commit:     e8e1041a0f579d133d77810e49d3dbd4b59f559f
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Feb 11 21:48:47 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Feb 11 21:48:47 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=e8e1041a

sci-biology/grass: add DEPENDency on sys-cluster/openmpi

Package-Manager: portage-2.2.26

 sci-biology/grass/grass-20130628.ebuild | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/sci-biology/grass/grass-20130628.ebuild b/sci-biology/grass/grass-20130628.ebuild
index d591da6..a89aca5 100644
--- a/sci-biology/grass/grass-20130628.ebuild
+++ b/sci-biology/grass/grass-20130628.ebuild
@@ -19,7 +19,8 @@ IUSE=""
 # ilcplex/ilocplex.h: No such file or directory
 # https://github.com/AlexeyG/GRASS/issues/6
 DEPEND="sci-biology/bamtools
-	sci-biology/ncbi-tools++"
+	sci-biology/ncbi-tools++
+	sys-cluster/openmpi"
 RDEPEND="${DEPEND}"
 
 S="${WORKDIR}"/GRASS-master