Import from Science overlay

Package-Manager: portage-2.2.0_alpha74/cvs/Linux x86_64

4 files changed, 85 insertions, 0 deletions

diff --git a/sci-biology/bamtools/ChangeLog b/sci-biology/bamtools/ChangeLog
new file mode 100644
index 000000000000..83257ba67c99
--- /dev/null
+++ b/sci-biology/bamtools/ChangeLog
@@ -0,0 +1,24 @@
+# ChangeLog for sci-biology/bamtools
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/bamtools/ChangeLog,v 1.1 2012/02/25 17:46:03 weaver Exp $
+
+  25 Feb 2012; Andrey Kislyuk <weaver@gentoo.org> +bamtools-1.0.2.ebuild,
+  +metadata.xml:
+  Import from Science overlay
+
+*bamtools-1.0.2 (10 Sep 2011)
+
+  10 Sep 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  +bamtools-1.0.2.ebuild, bamtools-9999.ebuild, -bamtools-20101215.ebuild,
+  metadata.xml:
+  moved to new release download link and version bump, documented that included
+  JsonCPP is a modified version bamtools-20101215.ebuild bamtools-1.0.2.ebuild
+  bamtools-9999.ebuild
+
+  08 Sep 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  bamtools-9999.ebuild, bamtools-20101215.ebuild:
+  Point to current HOMEPAGE bamtools-20101215.ebuild bamtools-9999.ebuild
+
+  24 Jun 2011; Justin Lecher <jlec@gentoo.org> bamtools-9999.ebuild:
+  Moved from 'git' to 'git-2'
+
diff --git a/sci-biology/bamtools/Manifest b/sci-biology/bamtools/Manifest
new file mode 100644
index 000000000000..8556e3f24d04
--- /dev/null
+++ b/sci-biology/bamtools/Manifest
@@ -0,0 +1,14 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA1
+
+DIST bamtools-1.0.2.tar.gz 207523 RMD160 ba737ad591c69d9110138dc066b9c2133ef77bb4 SHA1 70d4a1f8d7da73dd381b609b618ed19b6184366e SHA256 d3ca75d2bec531f15dbc400a76afbe48d47452ce05552c88943bbce81a0862d8
+EBUILD bamtools-1.0.2.ebuild 946 RMD160 b884895dc208cb71aa0f254e56c98e51012a3b6b SHA1 8ec28ea29475d4e557cd26fff81d29a24203ef62 SHA256 05250fa2ed07cfe5acdf8ecbfe93c327b1fde13f13ef73d16d2ed351f97557fa
+MISC ChangeLog 985 RMD160 2a09b05dc6198a2938029acf2949f73bd30dec46 SHA1 f86b2c7eae147a2984b7f457a49b3564e1d9401f SHA256 bb413fcbacc83076199fa1af1bc980f532844ee3b8ae91aa4a5207aa35175a12
+MISC metadata.xml 649 RMD160 8a5dce94c7b1d2c3d4a65514ab4596575d10fdb7 SHA1 9340ab0bbe312b008e3084a2fe640ea3fb28ecfe SHA256 ef2022465e51bcfb97cd3c02a93ce3c94826d059f444aacccc75c33281488f94
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v1.4.11 (GNU/Linux)
+
+iEYEARECAAYFAk9JHmEACgkQ8xSwyhbn2OYOZwCfRGbmpn57MDDZfWd52Jdsw0Wu
+410AoLUdIuw90iRGZX+uyRr16KOvhxsp
+=/sn6
+-----END PGP SIGNATURE-----
diff --git a/sci-biology/bamtools/bamtools-1.0.2.ebuild b/sci-biology/bamtools/bamtools-1.0.2.ebuild
new file mode 100644
index 000000000000..7017a38a6e11
--- /dev/null
+++ b/sci-biology/bamtools/bamtools-1.0.2.ebuild
@@ -0,0 +1,33 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/bamtools/bamtools-1.0.2.ebuild,v 1.1 2012/02/25 17:46:03 weaver Exp $
+
+EAPI=4
+
+inherit cmake-utils
+
+DESCRIPTION="BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files."
+HOMEPAGE="https://github.com/pezmaster31/bamtools"
+SRC_URI="https://github.com/downloads/pezmaster31/bamtools/"${P}".tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND="sys-libs/zlib"
+RDEPEND="${DEPEND}"
+
+src_install() {
+	for i in bin/bamtools-${PV} lib/libbamtools.so.${PV} lib/libbamtools-utils.so.${PV}; do
+		TMPDIR="$(pwd)" scanelf -Xr $i || die
+	done
+
+	dobin bin/bamtools || die
+	dolib lib/* || die
+	insinto /usr/include/bamtools/api || die
+	doins include/api/* || die
+	insinto /usr/include/bamtools/shared || die
+	doins include/shared/*
+	dodoc README || die
+}
diff --git a/sci-biology/bamtools/metadata.xml b/sci-biology/bamtools/metadata.xml
new file mode 100644
index 000000000000..09f78c98d172
--- /dev/null
+++ b/sci-biology/bamtools/metadata.xml
@@ -0,0 +1,14 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<herd>sci-biology</herd>
+	<maintainer>
+		<email>weaver@gentoo.org</email>
+		<name>Andrey Kislyuk</name>
+	</maintainer>
+	<maintainer>
+		<email>mmokrejs@fold.natur.cuni.cz</email>
+		<name>Martin Mokrejs</name>
+	</maintainer>
+	<longdescription>BAM (Binary Alignment/Map) format is useful for storing large DNA sequence alignments. It is closely related to the text-based SAM format, but optimized for random-access. BamTools provides a fast, flexible C++ API for reading and writing BAM files.</longdescription>
+</pkgmetadata>