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>[email protected]</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>
