* [gentoo-commits] proj/sci:master commit in: sci-biology/brat_bw/
@ 2016-09-01 9:52 99% Martin Mokrejs
0 siblings, 0 replies; 1+ results
From: Martin Mokrejs @ 2016-09-01 9:52 UTC (permalink / raw
To: gentoo-commits
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-biology@gentoo.org</email>
+ <name>Gentoo Biology Project</name>
+ </maintainer>
+ </pkgmetadata>
^ permalink raw reply related [relevance 99%]
Results 1-1 of 1 | reverse | options above
-- pct% links below jump to the message on this page, permalinks otherwise --
2016-09-01 9:52 99% [gentoo-commits] proj/sci:master commit in: sci-biology/brat_bw/ Martin Mokrejs
This is a public inbox, see mirroring instructions
for how to clone and mirror all data and code used for this inbox