commit: 7f516dcc0ff31783264d5aa43b598564d6dd5d1a Author: David Seifert <soap <AT> gentoo <DOT> org> AuthorDate: Sat Sep 2 08:11:47 2017 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Sat Sep 2 08:11:47 2017 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=7f516dcc
sci-biology/bwa: Latest in main tree sci-biology/bwa/bwa-0.7.16.ebuild | 36 ------------------------- sci-biology/bwa/files/bwa-0.7.15-Makefile.patch | 27 ------------------- sci-biology/bwa/metadata.xml | 11 -------- 3 files changed, 74 deletions(-) diff --git a/sci-biology/bwa/bwa-0.7.16.ebuild b/sci-biology/bwa/bwa-0.7.16.ebuild deleted file mode 100644 index 1568adff3..000000000 --- a/sci-biology/bwa/bwa-0.7.16.ebuild +++ /dev/null @@ -1,36 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit 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/${P}.tar.bz2" - -LICENSE="GPL-3" -SLOT="0" -IUSE="" -KEYWORDS="~amd64 ~x86 ~x64-macos" - -RDEPEND="dev-lang/perl" - -DOCS=( NEWS.md README-alt.md README.md ) -PATCHES=( "${FILESDIR}"/${PN}-0.7.15-Makefile.patch ) - -src_configure() { - tc-export CC AR - default -} - -src_install() { - dobin bwa - - doman bwa.1 - - exeinto /usr/libexec/${PN} - doexe qualfa2fq.pl xa2multi.pl - - einstalldocs -} diff --git a/sci-biology/bwa/files/bwa-0.7.15-Makefile.patch b/sci-biology/bwa/files/bwa-0.7.15-Makefile.patch deleted file mode 100644 index 39b437a02..000000000 --- a/sci-biology/bwa/files/bwa-0.7.15-Makefile.patch +++ /dev/null @@ -1,27 +0,0 @@ ---- bwa-0.7.13/Makefile -+++ bwa-0.7.13/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 ceb43ead2..000000000 --- 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-biol...@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="sourceforge">bio-bwa</remote-id> - </upstream> -</pkgmetadata>
