Import from Science overlay

Package-Manager: portage-2.2_rc20/cvs/Linux 2.6.26-gentoo-r4 x86_64

5 files changed, 97 insertions, 0 deletions

diff --git a/sci-biology/lagan/ChangeLog b/sci-biology/lagan/ChangeLog
new file mode 100644
index 000000000000..c48f7c0d4655
--- /dev/null
+++ b/sci-biology/lagan/ChangeLog
@@ -0,0 +1,13 @@
+# ChangeLog for sci-biology/lagan
+# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/lagan/ChangeLog,v 1.1 2009/02/27 00:23:49 weaver Exp $
+
+*lagan-2.0 (26 Feb 2009)
+
+  26 Feb 2009; Andrey Kislyuk <weaver@gentoo.org>
+  +files/lagan-2.0-gcc4.3.patch, +metadata.xml, +lagan-2.0.ebuild:
+  Import from Science overlay
+
+  04 Feb 2009; weaver <weaver@gentoo.org> ChangeLog:
+  New package sci-biology/lagan, bug 257667
+
diff --git a/sci-biology/lagan/Manifest b/sci-biology/lagan/Manifest
new file mode 100644
index 000000000000..422a894f234a
--- /dev/null
+++ b/sci-biology/lagan/Manifest
@@ -0,0 +1,5 @@
+AUX lagan-2.0-gcc4.3.patch 821 RMD160 2334def85c5859c4ceabc91f997843465a2d89b6 SHA1 1aeeb1a585f70fcad08688e1fbee9e0b626337a5 SHA256 e0575359288e7de97d35a7cce7b92c5619d2f75026beefc9139042280aa20a22
+DIST lagan20.tar.gz 589115 RMD160 a55680c95efc84a4cdc21508223fd0f9bc934f98 SHA1 592ca7e92c7307861e4b2bb66820d1dce1663376 SHA256 a65e61ed4fd6608f4e5ad5b11a1b77f4fec1a207d822c5885b3e86727496e1fe
+EBUILD lagan-2.0.ebuild 1305 RMD160 6c7e4082083c1751f66b5dd1c333982d3383a881 SHA1 5b0f0e572d4b4b90f82beb00629ec1e25f978d8e SHA256 ed6010d84c218bfa29ade15da142aefce476e69ad5bc7b19428334c455a0362b
+MISC ChangeLog 479 RMD160 5b98cefeae1b02befb72171124d26aa0252fca29 SHA1 240bda6b9c942b53d26d7b4834af2d1cfb737d1e SHA256 24120bf8e45a4675c938bb1b788bcf5c8da805be2dc98c3513820df628c89cb2
+MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110
diff --git a/sci-biology/lagan/files/lagan-2.0-gcc4.3.patch b/sci-biology/lagan/files/lagan-2.0-gcc4.3.patch
new file mode 100644
index 000000000000..a4b1d6808e2f
--- /dev/null
+++ b/sci-biology/lagan/files/lagan-2.0-gcc4.3.patch
@@ -0,0 +1,23 @@
+diff -durr lagan20-orig/src/glocal/score.cpp lagan20/src/glocal/score.cpp
+--- lagan20-orig/src/glocal/score.cpp	2009-02-04 15:25:57.698333297 +0000
++++ lagan20/src/glocal/score.cpp	2009-02-04 15:27:23.894092890 +0000
+@@ -2,7 +2,7 @@
+ #include<score.h>
+ #include<leftinfluence.h>
+ #include<rightinfluence.h>
+-#include<fstream.h>
++#include<fstream>
+ 
+ extern vector<class Score*> scoreFunctions[1<<(UPSTRANDBITS+DOWNSTRANDBITS+RELPOSBITS)];
+ 
+diff -durr lagan20-orig/src/utils/Glue.cpp lagan20/src/utils/Glue.cpp
+--- lagan20-orig/src/utils/Glue.cpp	2009-02-04 15:25:57.702333182 +0000
++++ lagan20/src/utils/Glue.cpp	2009-02-04 15:27:04.190822654 +0000
+@@ -1,6 +1,7 @@
+ #include "MultiSequence.h"
+ #include "SafeVector.h"
+ #include "Output.h"
++#include <string.h>
+ #include <math.h>
+ #include <assert.h>
+ #include <fstream>
diff --git a/sci-biology/lagan/lagan-2.0.ebuild b/sci-biology/lagan/lagan-2.0.ebuild
new file mode 100644
index 000000000000..79049af85ace
--- /dev/null
+++ b/sci-biology/lagan/lagan-2.0.ebuild
@@ -0,0 +1,47 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/lagan/lagan-2.0.ebuild,v 1.1 2009/02/27 00:23:49 weaver Exp $
+
+inherit eutils
+
+MY_PV="20"
+
+DESCRIPTION="LAGAN, Multi-LAGAN, Shuffle-LAGAN, Supermap: Whole-genome multiple alignment of genomic DNA"
+HOMEPAGE="http://lagan.stanford.edu/lagan_web/index.shtml"
+SRC_URI="http://lagan.stanford.edu/lagan_web/lagan${MY_PV}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 ~x86"
+
+DEPEND=""
+RDEPEND=""
+
+S="${WORKDIR}/lagan${MY_PV}"
+
+src_unpack() {
+	unpack ${A}
+	sed -i "/use Getopt::Long;/ i use lib \"/usr/share/${PN}/lib\";" "${S}/supermap.pl" || die
+	epatch "${FILESDIR}"/${P}-*.patch
+}
+
+src_install() {
+	dobin lagan.pl slagan.pl mlagan
+	rm lagan.pl slagan.pl utils/Utils.pm
+	dodir /usr/share/${PN}/lib
+	insinto /usr/share/${PN}/lib
+	doins Utils.pm
+	exeinto /usr/share/${PN}/utils
+	doexe utils/*
+	exeinto /usr/share/${PN}
+	doexe *.pl anchors chaos glocal order prolagan
+	insinto /usr/share/${PN}
+	doins *.txt
+	dosym /usr/share/${PN}/supermap.pl /usr/bin/supermap
+	dosym /usr/bin/lagan.pl /usr/bin/lagan
+	dosym /usr/bin/slagan.pl /usr/bin/slagan
+	echo "LAGAN_DIR=\"/usr/share/${PN}\"" > ${S}/99${PN}
+	doenvd "${S}/99${PN}"
+	dodoc Readmes/README.*
+}
diff --git a/sci-biology/lagan/metadata.xml b/sci-biology/lagan/metadata.xml
new file mode 100644
index 000000000000..3302123e5718
--- /dev/null
+++ b/sci-biology/lagan/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer>
+		<email>weaver@gentoo.org</email>
+		<name>Andrey Kislyuk</name>
+	</maintainer>
+	<herd>sci-biology</herd>
+</pkgmetadata>