commit: 6921d365bb6816d75863475baa434d02feec8048 Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Sun Feb 19 19:39:05 2017 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Sun Feb 19 19:39:05 2017 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=6921d365
sci-biology/sambamba: multithreaded tool written in D language The ebuilds are incomplete as I need to figure out how to compile the thingie. Make does not exit upon error (released tarball does not contain htslib/). Package-Manager: Portage-2.3.3, Repoman-2.3.1 sci-biology/sambamba/metadata.xml | 12 +++++++++++ sci-biology/sambamba/sambamba-0.6.5.ebuild | 32 ++++++++++++++++++++++++++++++ sci-biology/sambamba/sambamba-9999.ebuild | 27 +++++++++++++++++++++++++ 3 files changed, 71 insertions(+) diff --git a/sci-biology/sambamba/metadata.xml b/sci-biology/sambamba/metadata.xml new file mode 100644 index 000000000..f68a1b6fa --- /dev/null +++ b/sci-biology/sambamba/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> +<pkgmetadata> + <maintainer type="person"> + <email>[email protected]</email> + <name>Martin Mokrejs</name> + </maintainer> + <maintainer type="project"> + <email>[email protected]</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/sambamba/sambamba-0.6.5.ebuild b/sci-biology/sambamba/sambamba-0.6.5.ebuild new file mode 100644 index 000000000..49a7cb0bb --- /dev/null +++ b/sci-biology/sambamba/sambamba-0.6.5.ebuild @@ -0,0 +1,32 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=6 + +DESCRIPTION="Parallell process SAM/BAM/CRAM files faster than samtools" +HOMEPAGE="http://lomereiter.github.io/sambamba"; +SRC_URI="https://github.com/lomereiter/sambamba/archive/v0.6.5.tar.gz -> ${P}.tar.gz" + +LICENSE="GPL-2+" +SLOT="0" +KEYWORDS="" +IUSE="debug" + +# needs ldmd2 compiler from LDC package +# wget https://github.com/ldc-developers/ldc/releases/download/v0.17.1/ldc2-0.17.1-linux-x86_64.tar.xz +# tar xJf ldc2-0.17.1-linux-x86_64.tar.xz +# export PATH=~/ldc2-0.17.1-linux-x86_64/bin/:$PATH +# export LIBRARY_PATH=~/ldc2-0.17.1-linux-x86_64/lib/ +# +# contains bundled htslib +DEPEND="" +RDEPEND="${DEPEND}" + +src_compile(){ + if use debug ; then + emake sambamba-ldmd2-debug + else + emake sambamba-ldmd2-64 + fi +} diff --git a/sci-biology/sambamba/sambamba-9999.ebuild b/sci-biology/sambamba/sambamba-9999.ebuild new file mode 100644 index 000000000..c19a5053f --- /dev/null +++ b/sci-biology/sambamba/sambamba-9999.ebuild @@ -0,0 +1,27 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=6 + +inherit git-r3 + +DESCRIPTION="Parallell process SAM/BAM/CRAM files faster than samtools" +HOMEPAGE="http://lomereiter.github.io/sambamba"; +EGIT_REPO_URI="https://github.com/lomereiter/sambamba.git"; + +LICENSE="GPL-2+" +SLOT="0" +KEYWORDS="" +IUSE="debug" + +DEPEND="" +RDEPEND="${DEPEND}" + +src_compile(){ + if use debug ; then + emake sambamba-ldmd2-debug + else + emake sambamba-ldmd2-64 + fi +}
