commit: e8031d7da1b7dd9040cd4876c146f2190fc3734a Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Fri Mar 13 16:22:43 2015 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Fri Mar 13 16:22:43 2015 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=e8031d7d
new package; the k-mer size is set during compilation, use 'k=121 emerge kmergenie' to set your k-mer size Package-Manager: portage-2.2.15 sci-biology/kmergenie/ChangeLog | 10 +++++++ sci-biology/kmergenie/kmergenie-1.6950.ebuild | 40 +++++++++++++++++++++++++++ sci-biology/kmergenie/metadata.xml | 9 ++++++ 3 files changed, 59 insertions(+) diff --git a/sci-biology/kmergenie/ChangeLog b/sci-biology/kmergenie/ChangeLog new file mode 100644 index 0000000..482c032 --- /dev/null +++ b/sci-biology/kmergenie/ChangeLog @@ -0,0 +1,10 @@ +# ChangeLog for sci-biology/kmergenie +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*kmergenie-1.6950 (13 Mar 2015) + + 13 Mar 2015; Martin Mokrejs <[email protected]> + +kmergenie-1.6950.ebuild, +metadata.xml: + new package; the k-mer size is set during compilation, use 'k=121 emerge + kmergenie' to set your k-mer size diff --git a/sci-biology/kmergenie/kmergenie-1.6950.ebuild b/sci-biology/kmergenie/kmergenie-1.6950.ebuild new file mode 100644 index 0000000..91abe45 --- /dev/null +++ b/sci-biology/kmergenie/kmergenie-1.6950.ebuild @@ -0,0 +1,40 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit eutils + +PYTHON_COMPAT=( python{2_6,2_7} ) + +DESCRIPTION="Estimate best k-mer length to be used in novo assemblies (default set during compilation is 121)" +HOMEPAGE="http://kmergenie.bx.psu.edu/"; +SRC_URI="http://kmergenie.bx.psu.edu/"${P}".tar.gz"; + +LICENSE="CeCILL-1.1" +SLOT="0" +KEYWORDS="~amd64" +IUSE="" + +DEPEND="dev-lang/R" +RDEPEND="${DEPEND}" + +# Type `make` in the KmerGenie directory +# To enable larger values of k, e.g. 200, type `make clean ; make k=200`. +# +# usage: ./kmergenie reads_file + +src_prepare(){ + sed -e 's#-O4##' -i makefile || die +} + +src_compile(){ + make -j 1 || die +} + +src_install(){ + dobin kmergenie + dodoc README + # TODO: install also the python files +} diff --git a/sci-biology/kmergenie/metadata.xml b/sci-biology/kmergenie/metadata.xml new file mode 100644 index 0000000..2bc8930 --- /dev/null +++ b/sci-biology/kmergenie/metadata.xml @@ -0,0 +1,9 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> +<pkgmetadata> + <herd>sci-biology</herd> + <maintainer> + <email>[email protected]</email> + <name>Martin Mokrejs</name> + </maintainer> +</pkgmetadata>
