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

[Martin Mokrejs]

commit:     ae8cd41f5303f3507f0b77e67c46c3ca3b0d62d1
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Apr 30 23:19:25 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Apr 30 23:19:25 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=ae8cd41f

sci-biology/reptile: new package

Package-Manager: portage-2.2.18

 sci-biology/reptile/ChangeLog          |  9 ++++++++
 sci-biology/reptile/metadata.xml       |  9 ++++++++
 sci-biology/reptile/reptile-1.1.ebuild | 41 ++++++++++++++++++++++++++++++++++
 3 files changed, 59 insertions(+)

diff --git a/sci-biology/reptile/ChangeLog b/sci-biology/reptile/ChangeLog
new file mode 100644
index 0000000..bf348f8
--- /dev/null
+++ b/sci-biology/reptile/ChangeLog
@@ -0,0 +1,9 @@
+# ChangeLog for sci-biology/reptile
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*reptile-1.1 (30 Apr 2015)
+
+  30 Apr 2015; Martin Mokrejs <mmokrejs@×××××××××××××××.cz> +metadata.xml,
+  +reptile-1.1.ebuild:
+  sci-biology/reptile: new package

diff --git a/sci-biology/reptile/metadata.xml b/sci-biology/reptile/metadata.xml
new file mode 100644
index 0000000..2bc8930
--- /dev/null
+++ b/sci-biology/reptile/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@×××××××××××××××.cz</email>
+    <name>Martin Mokrejs</name>
+  </maintainer>
+</pkgmetadata>

diff --git a/sci-biology/reptile/reptile-1.1.ebuild b/sci-biology/reptile/reptile-1.1.ebuild
new file mode 100644
index 0000000..fd6ec77
--- /dev/null
+++ b/sci-biology/reptile/reptile-1.1.ebuild
@@ -0,0 +1,41 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+DESCRIPTION="Illumina read corrector"
+HOMEPAGE="http://aluru-sun.ece.iastate.edu/doku.php?id=reptile"
+SRC_URI="http://aluru-sun.ece.iastate.edu/lib/exe/fetch.php?media=source:reptile-v${PV}.zip -> "${PN}"-v"${PV}".zip"
+
+LICENSE="LGPL-3 GPL-3 Boost-1.0"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}
+	dev-lang/perl"
+
+S="${WORKDIR}"/"${PN}"-v"${PV}"
+
+src_prepare(){
+	sed -e 's#-Wall -O3#$(CXXFLAGS)#' -i src/makefile || die
+	sed -e 's#-Wall -O3#$(CXXFLAGS)#' -i utils/reptile_merger/makefile || die
+	sed -e 's#-Wall -O3#$(CXXFLAGS)#' -i utils/seq-analy/makefile || die
+}
+
+src_compile(){
+	cd src || die
+	emake all
+	cd ../utils/reptile_merger || die
+	emake all
+	cd ../seq-analy || die
+	emake all
+}
+
+src_install(){
+	newbin src/reptile-v1.1 reptile
+	dobin utils/reptile_merger/reptile_merger
+	dobin utils/fastq-converter-v2.0.pl
+}