sci-biology/reptile: new package

Package-Manager: portage-2.2.18

4 files changed, 60 insertions, 0 deletions

diff --git a/sci-biology/reptile/ChangeLog b/sci-biology/reptile/ChangeLog
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+++ b/sci-biology/reptile/ChangeLog
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+# 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@fold.natur.cuni.cz> +metadata.xml,
+  +reptile-1.1.ebuild:
+  sci-biology/reptile: new package
diff --git a/sci-biology/reptile/Manifest b/sci-biology/reptile/Manifest
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index 000000000..4e1ed40f6
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+++ b/sci-biology/reptile/Manifest
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+DIST reptile-v1.1.zip 79227 SHA256 400e30238599bc64320e1fd5c0b37a517a55e242458afc334bbf2f7dea5eb781 SHA512 ca397671d16e718926f61f8671920cff06f0ec458c63987361dc4c1b8b0742ee94759b22786ab3c8176238078a0d571d5b33edf805b176d8967a331a505c6d0e WHIRLPOOL 4b3342b9f1c3391c47c8ad761406d9cf81122df8231778243d81e2f377cce58c25d6cfee108e11ab69459cd51aff1121fa02dfce99419d14225f1d30a2ded062
diff --git a/sci-biology/reptile/metadata.xml b/sci-biology/reptile/metadata.xml
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+++ b/sci-biology/reptile/metadata.xml
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+<?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/reptile/reptile-1.1.ebuild b/sci-biology/reptile/reptile-1.1.ebuild
new file mode 100644
index 000000000..fd6ec7741
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+++ b/sci-biology/reptile/reptile-1.1.ebuild
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+# 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
+}