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| author |   Linlin Yan <yanlinlin82@gmail.com> | 2014-12-20 16:14:04 +0800 |
|---|---|---|
| committer | Linlin Yan <yanlinlin82@gmail.com> | 2014-12-20 16:14:04 +0800 |
| commit | 1ecaad76c11f5dce7a466addc22a17fe325a06b4 (patch) | |
| tree | ba51834830ef62840061d5e64c677887cad9f0d8 /sci-biology/bismark | |
| parent | sci-chemistry/freeon-9999: Move files. (diff) | |
| download | sci-1ecaad76c11f5dce7a466addc22a17fe325a06b4.tar.gz sci-1ecaad76c11f5dce7a466addc22a17fe325a06b4.tar.bz2 sci-1ecaad76c11f5dce7a466addc22a17fe325a06b4.zip | |
sci-biology/bismark: Add new package.
Diffstat (limited to 'sci-biology/bismark')
| -rw-r--r-- | sci-biology/bismark/Manifest | 1 | ||||
| -rw-r--r-- | sci-biology/bismark/bismark-0.13.0.ebuild | 32 | ||||
| -rw-r--r-- | sci-biology/bismark/metadata.xml | 18 |
3 files changed, 51 insertions, 0 deletions
diff --git a/sci-biology/bismark/Manifest b/sci-biology/bismark/Manifest new file mode 100644 index 000000000..c3ef5614e --- /dev/null +++ b/sci-biology/bismark/Manifest @@ -0,0 +1 @@ +DIST bismark_v0.13.0.tar.gz 1667188 SHA256 4266e7ece19bde693e9a0c15328eb3bde187031c168928a6e11ea2ba0ef95687 SHA512 5915e28a9647189d49c584cc0a90ee64ddd444e4acf9bc6c6ae25e1b01b18ab35ca1c3fa3b59834d641fa6c4a4b465d43f2908d3b23f1d45297d49323d3511c0 WHIRLPOOL d0e514dca8ffb8658194d63a067e9d131962e0c5c009cd9a026003ae9fa0befbc923935e0f81ece8c892f00925a7dbd27b65a55a0c040392caa83132a439bdf0 diff --git a/sci-biology/bismark/bismark-0.13.0.ebuild b/sci-biology/bismark/bismark-0.13.0.ebuild new file mode 100644 index 000000000..b62a44aa2 --- /dev/null +++ b/sci-biology/bismark/bismark-0.13.0.ebuild @@ -0,0 +1,32 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit toolchain-funcs + +DESCRIPTION="A tool to map bisulfite converted sequence reads and determine cytosine methylation states" +HOMEPAGE="http://www.bioinformatics.babraham.ac.uk/projects/bismark/" +SRC_URI="http://www.bioinformatics.babraham.ac.uk/projects/${PN}/${PN}_v${PV}.tar.gz" + +LICENSE="GPL-3+" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="+doc" + +DEPEND="" +RDEPEND="sci-biology/bowtie" + +S="${WORKDIR}/${PN}_v${PV}" + +src_install() { + dobin bismark{,2bedGraph,2report,_genome_preparation,_methylation_extractor} coverage2cytosine deduplicate_bismark + dodir /usr/share/${P} + insinto /usr/share/${P} + doins bismark_sitrep.tpl + dosym /usr/share/${P}/bismark_sitrep.tpl /usr/bin/bismark_sitrep.tpl + if use doc; then + dodoc Bismark_User_Guide.pdf RRBS_Guide.pdf license.txt RELEASE_NOTES.txt + fi +} diff --git a/sci-biology/bismark/metadata.xml b/sci-biology/bismark/metadata.xml new file mode 100644 index 000000000..12d2ae01b --- /dev/null +++ b/sci-biology/bismark/metadata.xml @@ -0,0 +1,18 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer> + <email>yanlinlin82@gmail.com</email> + <name>Linlin Yan</name> + </maintainer> + <herd>sci-biology</herd> + <longdescription lang="en"> +Bismark is a program to map bisulfite treated sequencing reads to a genome of interest and perform methylation calls in a single step. The output can be easily imported into a genome viewer, such as SeqMonk, and enables a researcher to analyse the methylation levels of their samples straight away. It's main features are: + +Bisulfite mapping and methylation calling in one single step +Supports single-end and paired-end read alignments +Supports ungapped and gapped alignments +Alignment seed length, number of mismatches etc. are adjustable +Output discriminates between cytosine methylation in CpG, CHG and CHH context + </longdescription> +</pkgmetadata> |