From: "git@oystercatcher mirror+tproxy" <git@oystercatcher.gentoo.org>
To: gentoo-commits@lists.gentoo.org
Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/bwa/files/, sci-biology/bwa/
Date: Tue, 3 Mar 2015 15:17:09 +0000 (UTC) [thread overview]
Message-ID: <1425395818.de8eb4ef90bedc116258edad0d769d7469dbc28c.git@gentoo> (raw)
commit: de8eb4ef90bedc116258edad0d769d7469dbc28c
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Mar 3 15:16:58 2015 +0000
Commit: git@oystercatcher mirror+tproxy <git <AT> oystercatcher <DOT> gentoo <DOT> org>
CommitDate: Tue Mar 3 15:16:58 2015 +0000
URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=de8eb4ef
IMport to CVS
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
sci-biology/bwa/bwa-0.7.12.ebuild | 34 --------------------------------
sci-biology/bwa/files/bwa_Makefile.patch | 27 -------------------------
sci-biology/bwa/metadata.xml | 5 -----
3 files changed, 66 deletions(-)
diff --git a/sci-biology/bwa/bwa-0.7.12.ebuild b/sci-biology/bwa/bwa-0.7.12.ebuild
deleted file mode 100644
index 62488f3..0000000
--- a/sci-biology/bwa/bwa-0.7.12.ebuild
+++ /dev/null
@@ -1,34 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-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/${P}.tar.bz2"
-
-LICENSE="GPL-3"
-SLOT="0"
-IUSE=""
-KEYWORDS="~amd64 ~x86 ~x64-macos"
-
-PATCHES=( "${FILESDIR}"/${PN}_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_Makefile.patch b/sci-biology/bwa/files/bwa_Makefile.patch
deleted file mode 100644
index 406e9b0..0000000
--- a/sci-biology/bwa/files/bwa_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 f17a827..0000000
--- a/sci-biology/bwa/metadata.xml
+++ /dev/null
@@ -1,5 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <herd>sci-biology</herd>
-</pkgmetadata>
next reply other threads:[~2015-03-03 15:17 UTC|newest]
Thread overview: 4+ messages / expand[flat|nested] mbox.gz Atom feed top
2015-03-03 15:17 git@oystercatcher mirror+tproxy [this message]
-- strict thread matches above, loose matches on Subject: below --
2016-05-17 9:19 [gentoo-commits] proj/sci:master commit in: sci-biology/bwa/files/, sci-biology/bwa/ Marius Brehler
2017-07-31 11:26 Martin Mokrejs
2018-06-24 8:28 Martin Mokrejs
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