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

["Martin Mokrejs" <mmokrejs@fold.natur.cuni.cz>]

commit:     aeab720fe4e2a73d39d79fa4570cd71219f256f6
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat Feb 14 16:14:42 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat Feb 14 16:14:42 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=aeab720f

new package

Package-Manager: portage-2.2.15

---
 sci-biology/mip-scaffolder/ChangeLog               |  9 ++++++
 sci-biology/mip-scaffolder/metadata.xml            |  9 ++++++
 .../mip-scaffolder/mip-scaffolder-0.6.ebuild       | 32 ++++++++++++++++++++++
 3 files changed, 50 insertions(+)

diff --git a/sci-biology/mip-scaffolder/ChangeLog b/sci-biology/mip-scaffolder/ChangeLog
new file mode 100644
index 0000000..0cba1df
--- /dev/null
+++ b/sci-biology/mip-scaffolder/ChangeLog
@@ -0,0 +1,9 @@
+# ChangeLog for sci-biology/mip-scaffolder
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*mip-scaffolder-0.6 (14 Feb 2015)
+
+  14 Feb 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml,
+  +mip-scaffolder-0.6.ebuild:
+  new package

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

diff --git a/sci-biology/mip-scaffolder/mip-scaffolder-0.6.ebuild b/sci-biology/mip-scaffolder/mip-scaffolder-0.6.ebuild
new file mode 100644
index 0000000..525ecbe
--- /dev/null
+++ b/sci-biology/mip-scaffolder/mip-scaffolder-0.6.ebuild
@@ -0,0 +1,32 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit toolchain-funcs
+
+DESCRIPTION="Scaffold contigs using ABI Solid or Illumina mate pair info"
+HOMEPAGE="http://www.cs.helsinki.fi/u/lmsalmel/mip-scaffolder"
+SRC_URI="http://www.cs.helsinki.fi/u/lmsalmel/mip-scaffolder/"${P}".tar.gz"
+
+LICENSE="mip-scaffolder"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+DEPEND="sci-libs/lemon
+	sci-mathematics/lpsolve
+	dev-lang/perl"
+RDEPEND="${DEPEND}"
+
+src_prepare(){
+	sed -e 's:/home/user/lp-solve/:/usr/include/lpsolve/:; s:/home/user/lemon/:/usr/include/lemon:; s:/home/user/mip-scaffolder-0.6/:/usr/bin:' -i Makefile
+	find . -name Makefile | while read f; do sed -e "s:CC=g++:CC=$(tc-getCXX):; s:CFLAGS=-Wall -g -O9:CFLAGS=${CFLAGS}:" -i $f; done
+	sed -e 's:$(LPSOLVEROOT)/liblpsolve55.a:-llpsolve55:' -i split-scaffold/Makefile
+}
+
+src_install(){
+	dobin combine-scaffold/combine-scaffold filter-mappings/filter-mappings split-scaffold/split-scaffold write-scaffold/write-scaffold scripts/*.pl scripts/*.sh
+	dodoc README
+}