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>
