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)
