commit: a788b3a56fa7e60683c10ae8c8e73490d1575e0f Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Sun Mar 23 20:52:30 2014 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Sun Mar 23 20:52:30 2014 +0000 URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=a788b3a5
sci-biology/MaSuRCA: new package but with a missing LICENSE and needs tweak to get all configure's running --- sci-biology/MaSuRCA/MaSuRCA-2.1.0.ebuild | 63 ++++++++++++++++++++++++++++++++ sci-biology/MaSuRCA/metadata.xml | 9 +++++ 2 files changed, 72 insertions(+) diff --git a/sci-biology/MaSuRCA/MaSuRCA-2.1.0.ebuild b/sci-biology/MaSuRCA/MaSuRCA-2.1.0.ebuild new file mode 100644 index 0000000..28934c3 --- /dev/null +++ b/sci-biology/MaSuRCA/MaSuRCA-2.1.0.ebuild @@ -0,0 +1,63 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +DESCRIPTION="Assembler to combine Sanger, Roche 454 and Illumina Solexa reads" +HOMEPAGE="http://www.genome.umd.edu/masurca.html"; +SRC_URI="ftp://ftp.genome.umd.edu/pub/MaSuRCA/MaSuRCA-"${PV}".tar.gz + ftp://ftp.genome.umd.edu/pub/MaSuRCA/MaSuRCA_QuickStartGuide.pdf"; + +LICENSE="" +SLOT="0" +KEYWORDS="" +IUSE="" + +DEPEND="dev-lang/perl + app-arch/bzip2" +RDEPEND="${DEPEND}" + +# the ebuild mimics "${S}"/install.sh +src_configure(){ + cd jellyfish-1.1.11 || die + econf + + cd ../jellyfish-2.0.0rc1 || die + econf --program-suffix=-2.0 + + cd ../CA/kmer || die + sh ./configure.sh + econf + + cd ../../SuperReads-0.3.2 || die + econf + + cd ../quorum-0.3.2 || die + econf --enable-relative-paths --with-relative-jf-path +} + +src_compile(){ + cd jellyfish-1.1.11 || die + emake + + cd ../jellyfish-2.0.0rc1 || die + emake + + cd ../CA/kmer || die + emake + + cd ../../CA/src || die + emake + + cd ../SuperReads-0.3.2 || die + emake + + cd ../quorum-0.3.2 || die + emake +} + +src_install(){ + dobin masurca + dodoc sr_config_example.txt +} diff --git a/sci-biology/MaSuRCA/metadata.xml b/sci-biology/MaSuRCA/metadata.xml new file mode 100644 index 0000000..2bc8930 --- /dev/null +++ b/sci-biology/MaSuRCA/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>mmokr...@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> +</pkgmetadata>
