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| author |   Martin Mokrejš <mmokrejs@fold.natur.cuni.cz> | 2015-03-13 17:22:43 +0100 |
|---|---|---|
| committer | Martin Mokrejš <mmokrejs@fold.natur.cuni.cz> | 2015-03-13 17:22:43 +0100 |
| commit | e8031d7da1b7dd9040cd4876c146f2190fc3734a (patch) | |
| tree | b6ecccc6575742a1350a122e7239b76fe0394ea3 /sci-biology/kmergenie | |
| parent | install also the vcftools binaries although it should be a separate package (diff) | |
| download | sci-e8031d7da1b7dd9040cd4876c146f2190fc3734a.tar.gz sci-e8031d7da1b7dd9040cd4876c146f2190fc3734a.tar.bz2 sci-e8031d7da1b7dd9040cd4876c146f2190fc3734a.zip | |
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
Diffstat (limited to 'sci-biology/kmergenie')
| -rw-r--r-- | sci-biology/kmergenie/ChangeLog | 10 | ||||
| -rw-r--r-- | sci-biology/kmergenie/Manifest | 1 | ||||
| -rw-r--r-- | sci-biology/kmergenie/kmergenie-1.6950.ebuild | 40 | ||||
| -rw-r--r-- | sci-biology/kmergenie/metadata.xml | 9 |
4 files changed, 60 insertions, 0 deletions
diff --git a/sci-biology/kmergenie/ChangeLog b/sci-biology/kmergenie/ChangeLog new file mode 100644 index 000000000..482c03280 --- /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 <mmokrejs@fold.natur.cuni.cz> + +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/Manifest b/sci-biology/kmergenie/Manifest new file mode 100644 index 000000000..3fba4587a --- /dev/null +++ b/sci-biology/kmergenie/Manifest @@ -0,0 +1 @@ +DIST kmergenie-1.6950.tar.gz 423073 SHA256 5ca272253098886571a6044bf613e701775bd66b61e76d0260101e74c036b5da SHA512 2f12bd8cb3f374d25df278d244a546cc83f24b78e39d486ee8f1a731157c6c2b4d614c614c6bf1577e148a482c7eac5e11d3c36cdcf357ea29beb0ed4fa9e4bb WHIRLPOOL 2f1af8fda1c4d15e7e6bf3ec1bb4f342ca20455a319282987a197a1475afc73f97dc34049903328134250387b97ec56f9a9ccb59c697d4091f210821ea827119 diff --git a/sci-biology/kmergenie/kmergenie-1.6950.ebuild b/sci-biology/kmergenie/kmergenie-1.6950.ebuild new file mode 100644 index 000000000..91abe4573 --- /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 000000000..2bc893037 --- /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>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> +</pkgmetadata> |