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| author |   Justin Lecher <jlec@gentoo.org> | 2015-03-03 16:16:58 +0100 |
|---|---|---|
| committer | Justin Lecher <jlec@gentoo.org> | 2015-03-03 16:16:58 +0100 |
| commit | de8eb4ef90bedc116258edad0d769d7469dbc28c (patch) | |
| tree | df807a7a7caae455a3f5da20580573850d014f2b | |
| parent | app-doc/root-docs: 5.34.26 is now in portage (diff) | |
| download | sci-de8eb4ef90bedc116258edad0d769d7469dbc28c.tar.gz sci-de8eb4ef90bedc116258edad0d769d7469dbc28c.tar.bz2 sci-de8eb4ef90bedc116258edad0d769d7469dbc28c.zip | |
IMport to CVS
Signed-off-by: Justin Lecher <jlec@gentoo.org>
| -rw-r--r-- | sci-biology/bwa/Manifest | 1 | ||||
| -rw-r--r-- | sci-biology/bwa/bwa-0.7.12.ebuild | 34 | ||||
| -rw-r--r-- | sci-biology/bwa/files/bwa_Makefile.patch | 27 | ||||
| -rw-r--r-- | sci-biology/bwa/metadata.xml | 5 |
4 files changed, 0 insertions, 67 deletions
diff --git a/sci-biology/bwa/Manifest b/sci-biology/bwa/Manifest deleted file mode 100644 index 9c0d995bf..000000000 --- a/sci-biology/bwa/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST bwa-0.7.12.tar.bz2 184599 SHA256 701dcad147ae470d741717a72c369b338df7f80bff4bb8eee8176c66f16d608c SHA512 3ea093b861c1596d20b1ee0336468b66e52bc9f26e3d0bcbba0ddccc7fe9b1af2c7e1ed2a4e1366fe93fec348152becc126d5f4685dae54f05e6c582488b3abd WHIRLPOOL 4b8651dedf2e09980850e7212fc2a77dc86b06f708af2077cff28cc843858b15825a203e3e02e7728418e9eb539004404f7c4b234c1f65de6a7b7dfe4dcfd1d0 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 62488f328..000000000 --- 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 406e9b052..000000000 --- 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 f17a827e3..000000000 --- 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> |