commit: 541abbcdf09e9575c2e021f5261e29b0a76a0327 Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Thu Sep 1 09:52:01 2016 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Thu Sep 1 09:52:01 2016 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=541abbcd
sci-biology/brat_bw: new package, successor of sci-biology/brat Package-Manager: portage-2.3.0 sci-biology/brat_bw/brat_bw-2.0.1.ebuild | 36 ++++++++++++++++++++++++++++++++ sci-biology/brat_bw/metadata.xml | 8 +++++++ 2 files changed, 44 insertions(+) diff --git a/sci-biology/brat_bw/brat_bw-2.0.1.ebuild b/sci-biology/brat_bw/brat_bw-2.0.1.ebuild new file mode 100644 index 0000000..5060439 --- /dev/null +++ b/sci-biology/brat_bw/brat_bw-2.0.1.ebuild @@ -0,0 +1,36 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit toolchain-funcs + +DESCRIPTION="Bisulfite-aware short read mapper, FM-index, no InDel support" +HOMEPAGE="http://compbio.cs.ucr.edu/brat/"; +SRC_URI="http://compbio.cs.ucr.edu/brat/downloads/${P}.tar.gz"; + +LICENSE="GPL-3" +SLOT="0" +IUSE="" +KEYWORDS="~amd64 ~x86" + +DEPEND="" +RDEPEND="!sci-biology/brat" + +src_prepare() { + sed \ + -e "s:-Wl,-O1 : :g" \ + -e "s:g++:$(tc-getCXX):g" \ + -e "s:-O3:${CFLAGS} ${LDFLAGS}:g" \ + -e "s:-w:-Wall:g" \ + -i Makefile || die +} + +src_install() { + dobin brat_bw build_bw trim acgt-count remove-dupl convert_to_sam + # possible FILLE_COLLISION with sci-biology/brat (probably some binaries just do the same) + # dobin ${PN} ${PN}-large trim acgt-count ${PN}-large-build rev-compl check-strands remove-dupl convert-to-sam + dodoc README + newdoc {'User Manual BRAT_2_0_1.pdf','User_Manual_BRAT_2_0_1.pdf'} +} diff --git a/sci-biology/brat_bw/metadata.xml b/sci-biology/brat_bw/metadata.xml new file mode 100644 index 0000000..004c995 --- /dev/null +++ b/sci-biology/brat_bw/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biol...@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + </pkgmetadata>
