New package, ebuild written by me, dependency of sci-biology/GBrowse

Package-Manager: portage-2.2.0_alpha45/cvs/Linux x86_64

4 files changed, 68 insertions, 0 deletions

diff --git a/dev-perl/Bio-SamTools/Bio-SamTools-1.29.ebuild b/dev-perl/Bio-SamTools/Bio-SamTools-1.29.ebuild
new file mode 100644
index 000000000000..44499cf50933
--- /dev/null
+++ b/dev-perl/Bio-SamTools/Bio-SamTools-1.29.ebuild
@@ -0,0 +1,31 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/dev-perl/Bio-SamTools/Bio-SamTools-1.29.ebuild,v 1.1 2011/07/20 00:43:13 weaver Exp $
+
+EAPI=4
+
+MODULE_AUTHOR="LDS"
+inherit perl-module
+
+DESCRIPTION="Read SAM/BAM database files"
+
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND="sci-biology/bioperl
+	virtual/perl-ExtUtils-CBuilder
+	virtual/perl-Module-Build
+	sci-biology/samtools"
+RDEPEND="${DEPEND}"
+
+SRC_TEST=do
+
+src_prepare() {
+	sed -i -e 's|my $HeaderFile = "bam.h";|my $HeaderFile = "bam/bam.h";|' \
+		-e 's|my $LibFile    = "libbam.a";|my $LibFile    = "libbam.so";|' Build.PL || die
+	sed -i -e 's|#include "bam.h"|#include "bam/bam.h"|' \
+		-e 's|#include "khash.h"|#include "bam/khash.h"|' \
+		-e 's|#include "faidx.h"|#include "bam/faidx.h"|' lib/Bio/DB/Sam.xs || die
+	perl-module_src_prepare
+}
diff --git a/dev-perl/Bio-SamTools/ChangeLog b/dev-perl/Bio-SamTools/ChangeLog
new file mode 100644
index 000000000000..35caf5caf1c7
--- /dev/null
+++ b/dev-perl/Bio-SamTools/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for dev-perl/Bio-SamTools
+# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/dev-perl/Bio-SamTools/ChangeLog,v 1.1 2011/07/20 00:43:13 weaver Exp $
+
+*Bio-SamTools-1.29 (20 Jul 2011)
+
+  20 Jul 2011; Andrey Kislyuk <weaver@gentoo.org> +Bio-SamTools-1.29.ebuild,
+  +metadata.xml:
+  New package, ebuild written by me, dependency of sci-biology/GBrowse
+
diff --git a/dev-perl/Bio-SamTools/Manifest b/dev-perl/Bio-SamTools/Manifest
new file mode 100644
index 000000000000..b790e1250b39
--- /dev/null
+++ b/dev-perl/Bio-SamTools/Manifest
@@ -0,0 +1,14 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA1
+
+DIST Bio-SamTools-1.29.tar.gz 331127 RMD160 e86b51bdd7ffdfd42076da11b19ab4cbb3a9a93a SHA1 2925e95fc77d70d1bd5dedb3e1f4d7f00b8facd6 SHA256 9f9a6ea320b581a4bc4f61372f17310d063b3c1a534fd2f756e967c44b0f4c06
+EBUILD Bio-SamTools-1.29.ebuild 895 RMD160 373b65789b62760e624529da1f52ab02c67627e4 SHA1 dc603c98930112016ee7ef8f0dcfc289fed1eb1d SHA256 e501a24d8b8a1056c5f2a234b58d3fbbc1faa408437bf020212b7f96276933dc
+MISC ChangeLog 415 RMD160 834736b1ac7cebb2dedcf7e8ebb0175ae02d1030 SHA1 b5047a30c4e3fe744d377cabd303a831662094a8 SHA256 72777ddd2bbb47f9ff8b03b37119e5dbccd8fbd057e292c314feb53f35d49743
+MISC metadata.xml 357 RMD160 e313d1508f6c44d5532a952747d3ae64befb02d2 SHA1 d68a1814a6a44128c2059bc2504016ccbcecc6c8 SHA256 fd532c6a6e666788525911cf731239741f3bea9e22995e89d49b86c59a29a056
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v1.4.11 (GNU/Linux)
+
+iEYEARECAAYFAk4mJKcACgkQ8xSwyhbn2OadSACgpoN1dR53DekjQsndcdUfCDyD
+S6kAoKAGQXw5sPgKFH+eA4uE4wm4vcRO
+=atn/
+-----END PGP SIGNATURE-----
diff --git a/dev-perl/Bio-SamTools/metadata.xml b/dev-perl/Bio-SamTools/metadata.xml
new file mode 100644
index 000000000000..b0bab53dd025
--- /dev/null
+++ b/dev-perl/Bio-SamTools/metadata.xml
@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci</herd>
+  <herd>perl</herd>
+  <maintainer>
+    <email>weaver@gentoo.org</email>
+    <name>Andrey Kislyuk</name>
+  </maintainer>
+  <upstream>
+    <remote-id type="cpan">Bio-SamTools</remote-id>
+  </upstream>
+</pkgmetadata>