From: "Marius Brehler" <marbre@linux.sungazer.de>
To: gentoo-commits@lists.gentoo.org
Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/bwa/files/, sci-biology/bwa/
Date: Tue, 17 May 2016 09:19:11 +0000 (UTC) [thread overview]
Message-ID: <1462663243.1af3cb1d79a54e814b222cb56e4de3630136b828.marbre@gentoo> (raw)
commit: 1af3cb1d79a54e814b222cb56e4de3630136b828
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sat May 7 23:20:43 2016 +0000
Commit: Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
CommitDate: Sat May 7 23:20:43 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=1af3cb1d
sci-biology/bwa: move to main tree
sci-biology/bwa/bwa-0.7.13.ebuild | 36 -------------------------
sci-biology/bwa/files/bwa-0.7.13-Makefile.patch | 27 -------------------
sci-biology/bwa/metadata.xml | 11 --------
3 files changed, 74 deletions(-)
diff --git a/sci-biology/bwa/bwa-0.7.13.ebuild b/sci-biology/bwa/bwa-0.7.13.ebuild
deleted file mode 100644
index 27f314b..0000000
--- a/sci-biology/bwa/bwa-0.7.13.ebuild
+++ /dev/null
@@ -1,36 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-inherit eutils toolchain-funcs
-
-DESCRIPTION="Burrows-Wheeler Alignment Tool, a fast short genomic sequence aligner"
-HOMEPAGE="http://bio-bwa.sourceforge.net/"
-SRC_URI="mirror://sourceforge/bio-bwa/${P}.tar.bz2"
-
-LICENSE="GPL-3"
-# bwa-0.7.13 has "Apache2" branch with Apache2-licensed BWA with ropebwt2 index
-# feature which is slower than "bwtsw" algorithm but it has a permissive license.
-SLOT="0"
-IUSE=""
-KEYWORDS="~amd64 ~x86 ~x64-macos"
-
-PATCHES=( "${FILESDIR}"/${P}-Makefile.patch )
-
-src_prepare() {
- epatch ${PATCHES[@]}
- tc-export CC AR
-}
-
-src_install() {
- dobin bwa
-
- doman bwa.1
-
- exeinto /usr/libexec/${PN}
- doexe qualfa2fq.pl xa2multi.pl
-
- dodoc NEWS.md README-alt.md README.md
-}
diff --git a/sci-biology/bwa/files/bwa-0.7.13-Makefile.patch b/sci-biology/bwa/files/bwa-0.7.13-Makefile.patch
deleted file mode 100644
index 406e9b0..0000000
--- a/sci-biology/bwa/files/bwa-0.7.13-Makefile.patch
+++ /dev/null
@@ -1,27 +0,0 @@
---- Makefile
-+++ Makefile
-@@ -1,8 +1,8 @@
--CC= gcc
-+CC?= gcc
- #CC= clang --analyze
--CFLAGS= -g -Wall -Wno-unused-function -O2
-+CFLAGS?= -g -Wall -Wno-unused-function -O2
- WRAP_MALLOC=-DUSE_MALLOC_WRAPPERS
--AR= ar
-+AR?= ar
- DFLAGS= -DHAVE_PTHREAD $(WRAP_MALLOC)
- LOBJS= utils.o kthread.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o bwamem_extra.o malloc_wrap.o
- AOBJS= QSufSort.o bwt_gen.o bwashm.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o \
-@@ -26,10 +26,10 @@
- all:$(PROG)
-
- bwa:libbwa.a $(AOBJS) main.o
-- $(CC) $(CFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS)
-+ $(CC) $(CFLAGS) $(LDFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS)
-
- bwamem-lite:libbwa.a example.o
-- $(CC) $(CFLAGS) $(DFLAGS) example.o -o $@ -L. -lbwa $(LIBS)
-+ $(CC) $(CFLAGS) $(LDFLAGS) $(DFLAGS) example.o -o $@ -L. -lbwa $(LIBS)
-
- libbwa.a:$(LOBJS)
- $(AR) -csru $@ $(LOBJS)
diff --git a/sci-biology/bwa/metadata.xml b/sci-biology/bwa/metadata.xml
deleted file mode 100644
index ceb43ea..0000000
--- a/sci-biology/bwa/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?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>
- <upstream>
- <remote-id type="sourceforge">bio-bwa</remote-id>
- </upstream>
-</pkgmetadata>
next reply other threads:[~2016-05-17 9:19 UTC|newest]
Thread overview: 4+ messages / expand[flat|nested] mbox.gz Atom feed top
2016-05-17 9:19 Marius Brehler [this message]
-- strict thread matches above, loose matches on Subject: below --
2018-06-24 8:28 [gentoo-commits] proj/sci:master commit in: sci-biology/bwa/files/, sci-biology/bwa/ Martin Mokrejs
2017-07-31 11:26 Martin Mokrejs
2015-03-03 15:17 git@oystercatcher mirror+tproxy
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