[gentoo-commits] proj/sci:master commit in: sci-biology/biobambam2/

[Martin Mokrejs]

commit:     da6238be4b7a9b14122d501670264c61723f8235
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Jul 15 10:08:38 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Jul 15 10:08:38 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=da6238be

sci-biology/biobambam2: an updated package of sci-biology/biobambam, more ebuild tweaks

Package-Manager: portage-2.2.28

 sci-biology/biobambam2/biobambam2-9999.ebuild | 30 +++++++++++++++++++++++++++
 sci-biology/biobambam2/metadata.xml           | 21 +++++++++++++++++++
 2 files changed, 51 insertions(+)

diff --git a/sci-biology/biobambam2/biobambam2-9999.ebuild b/sci-biology/biobambam2/biobambam2-9999.ebuild
new file mode 100644
index 0000000..80e7206
--- /dev/null
+++ b/sci-biology/biobambam2/biobambam2-9999.ebuild
@@ -0,0 +1,30 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+inherit git-r3 autotools
+
+DESCRIPTION="Tools for bam file processing (libmaus2)"
+HOMEPAGE="https://github.com/gt1/biobambam2"
+EGIT_REPO_URI="https://github.com/gt1/biobambam2.git"
+
+LICENSE="GPL-3 MIT"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND="
+	!sci-biology/biobambam
+	>=sci-libs/libmaus2-2.0.225"
+RDEPEND="${DEPEND}"
+
+src_prepare() {
+	eautoreconf
+	eapply_user
+}
+
+src_configure(){
+	econf --with-libmaus2="${EPREFIX}"
+}

diff --git a/sci-biology/biobambam2/metadata.xml b/sci-biology/biobambam2/metadata.xml
new file mode 100644
index 0000000..a3e55a4
--- /dev/null
+++ b/sci-biology/biobambam2/metadata.xml
@@ -0,0 +1,21 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="project">
+    <email>sci-biology@g.o</email>
+    <name>Gentoo Biology Project</name>
+  </maintainer>
+  <longdescription lang="en">
+This package contains some tools for processing BAM files including
+
+bamcollate2: reads BAM and writes BAM reordered such that alignment or collated by query name
+bammarkduplicates: reads BAM and writes BAM with duplicate alignments marked using the BAM flags field
+bammaskflags: reads BAM and writes BAM while masking (removing) bits from the flags column
+bamrecompress: reads BAM and writes BAM with a defined compression setting. This tool is capable of multi-threading.
+bamsort: reads BAM and writes BAM resorted by coordinates or query name
+bamtofastq: reads BAM and writes FastQ; output can be collated or uncollated by query name
+</longdescription>
+  <upstream>
+    <remote-id type="github">gt1/biobambam</remote-id>
+  </upstream>
+</pkgmetadata>