commit: a4e405144f304e63344c5228e1407fdff6bfab75 Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Sun Apr 1 21:49:26 2018 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Sun Apr 1 21:49:26 2018 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=a4e40514
sci-biology/proovread: new package Will need more work from upstream to make it into Gentoo. Package-Manager: Portage-2.3.27, Repoman-2.3.9 sci-biology/proovread/metadata.xml | 12 +++++++ sci-biology/proovread/proovread-9999.ebuild | 50 +++++++++++++++++++++++++++++ 2 files changed, 62 insertions(+) diff --git a/sci-biology/proovread/metadata.xml b/sci-biology/proovread/metadata.xml new file mode 100644 index 000000000..138cb7705 --- /dev/null +++ b/sci-biology/proovread/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>mmokr...@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> + <maintainer type="project"> + <email>sci-biol...@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/proovread/proovread-9999.ebuild b/sci-biology/proovread/proovread-9999.ebuild new file mode 100644 index 000000000..11a78d2f8 --- /dev/null +++ b/sci-biology/proovread/proovread-9999.ebuild @@ -0,0 +1,50 @@ +# Copyright 1999-2018 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +[ "$PV" == "9999" ] && inherit git-r3 + +DESCRIPTION="Error correct PacBio subreads using Illumina reads" +HOMEPAGE="https://github.com/BioInf-Wuerzburg/proovread"; +if [ "$PV" == "9999" ]; then + EGIT_REPO_URI="https://github.com/BioInf-Wuerzburg/proovread"; + KEYWORDS="" +else + SRC_URI="" + KEYWORDS="~amd64 ~x86" # issue #125 +fi + +LICENSE="proovread" # Artistic-2.0 or GPL-3 but not for commercial +SLOT="0" +IUSE="" + +# needs Fasta::Parser +RDEPEND=" + >=dev-lang/perl-5.10 + dev-perl/Log-Log4perl + dev-perl/File-Which + >=sci-biology/ncbi-tools++-2.2.24 + >=sci-biology/samtools-1.1" +DEPEND="${RDEPEND} + >=sci-biology/shrimp-2 + sci-biology/blasr" + +src_install(){ + cd bin || die + dobin ChimeraToSeqFilter.pl dazz2sam ccseq bam2cns test_cfg.pl siamaera samfilter sam2cns proovread-flex proovread + cd ../util/bwa || die + dobin bwa-proovread # xa2multi.pl qualfa2fq.pl libbwa.a bwa.1 + cd ../../util/SeqFilter || die + dobin bin/SeqFilter + cd ../../util/SeqChunker || die + dobin bin/* + # cd ../util/blasr-1.3.1 || die + # dobin blasr + # dodoc LICENSE.txt +} + +pkg_postinst(){ + einfo "Proovread uses its own, modified version of bwa as bwa-proovread" + einfo "with linked in libbwa.a. It also bundles shrimp2 and blasr" +}
