[gentoo-commits] repo/gentoo:master commit in: sci-biology/bwa/files/, sci-biology/bwa/

[David Seifert]

commit:     59716472229d52eacd4bba26ac2d90a9b3f44233
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sat Sep  2 11:07:41 2017 +0000
Commit:     David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sat Sep  2 12:36:56 2017 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=59716472

sci-biology/bwa: Remove old

Package-Manager: Portage-2.3.8, Repoman-2.3.3
Closes: https://github.com/gentoo/gentoo/pull/5593

 sci-biology/bwa/Manifest                        |  2 --
 sci-biology/bwa/bwa-0.7.12.ebuild               | 33 -----------------------
 sci-biology/bwa/bwa-0.7.15.ebuild               | 36 -------------------------
 sci-biology/bwa/files/bwa-0.7.12-Makefile.patch | 27 -------------------
 4 files changed, 98 deletions(-)

diff --git a/sci-biology/bwa/Manifest b/sci-biology/bwa/Manifest
index d2daff2272e..e555b974c77 100644
--- a/sci-biology/bwa/Manifest
+++ b/sci-biology/bwa/Manifest
@@ -1,3 +1 @@
-DIST bwa-0.7.12.tar.bz2 184599 SHA256 701dcad147ae470d741717a72c369b338df7f80bff4bb8eee8176c66f16d608c SHA512 3ea093b861c1596d20b1ee0336468b66e52bc9f26e3d0bcbba0ddccc7fe9b1af2c7e1ed2a4e1366fe93fec348152becc126d5f4685dae54f05e6c582488b3abd WHIRLPOOL 4b8651dedf2e09980850e7212fc2a77dc86b06f708af2077cff28cc843858b15825a203e3e02e7728418e9eb539004404f7c4b234c1f65de6a7b7dfe4dcfd1d0
-DIST bwa-0.7.15.tar.bz2 189806 SHA256 2f56afefa49acc9bf45f12edb58e412565086cc20be098b8bf15ec07de8c0515 SHA512 cb862342aef1042751de55df095b4dac8344d9b41f00b0cca7f748829bf7fba71d15e4c7deaaa255eca6ee6af3ba58b370944ee702150cf17c29fb50ff25fa26 WHIRLPOOL 5d57d37339ff6c68c47ba0147ea21e4faa9a6cbbea2e66130e69bbb19802621ad22ae26889c06000109684961ed9d872605bffd469ddf97af2f1fdca3b8bd316
 DIST bwa-0.7.16a.tar.bz2 190773 SHA256 8fecdb5f88871351bbe050c18d6078121456c36ad75c5c78f33a926560ffc170 SHA512 8bbe223f79efd328d66adb88baf995e894f5944aad912ac1b464dc84dc9b4e22ddf77b60dcbe468e0eedc344ee58d08dc498777f0d2794a2c1e0ddd33dad606d WHIRLPOOL 624d94bb65fcfdbefa709f8e873b29f11d940c0ee54fc627a3305641bb15548de1162241ece07341623dae3b9970a49a7377dd0e634454cfef59a9c357f8b3ec

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 86f3d3e86c4..00000000000
--- a/sci-biology/bwa/bwa-0.7.12.ebuild
+++ /dev/null
@@ -1,33 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-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}"/${P}-Makefile.patch )
-
-src_prepare() {
-	epatch "${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/bwa-0.7.15.ebuild b/sci-biology/bwa/bwa-0.7.15.ebuild
deleted file mode 100644
index 0c8b90d357e..00000000000
--- a/sci-biology/bwa/bwa-0.7.15.ebuild
+++ /dev/null
@@ -1,36 +0,0 @@
-# Copyright 1999-2016 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}"/${P}-Makefile.patch )
-
-src_configure() {
-	tc-export CC AR
-	default
-}
-
-src_install() {
-	dobin bwa
-
-	doman bwa.1
-
-	exeinto /usr/libexec/${PN}
-	doexe qualfa2fq.pl xa2multi.pl
-
-	einstalldocs
-}

diff --git a/sci-biology/bwa/files/bwa-0.7.12-Makefile.patch b/sci-biology/bwa/files/bwa-0.7.12-Makefile.patch
deleted file mode 100644
index 406e9b05237..00000000000
--- a/sci-biology/bwa/files/bwa-0.7.12-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)