commit: 1a7c939f8f1087c8031e2621e53bd3bda0f043af Author: David Seifert <soap <AT> gentoo <DOT> org> AuthorDate: Sat Sep 26 10:00:48 2020 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Sat Sep 26 10:00:48 2020 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=1a7c939f
sci-biology/bwa: Remove old 0.7.16a Package-Manager: Portage-3.0.8, Repoman-3.0.1 Signed-off-by: David Seifert <soap <AT> gentoo.org> sci-biology/bwa/Manifest | 1 - sci-biology/bwa/bwa-0.7.16a.ebuild | 36 ------------------------- sci-biology/bwa/files/bwa-0.7.15-Makefile.patch | 27 ------------------- sci-biology/bwa/files/bwa-0.7.16a-gcc-10.patch | 7 ----- 4 files changed, 71 deletions(-) diff --git a/sci-biology/bwa/Manifest b/sci-biology/bwa/Manifest index 4b69e7f0403..5f912dc43cf 100644 --- a/sci-biology/bwa/Manifest +++ b/sci-biology/bwa/Manifest @@ -1,2 +1 @@ -DIST bwa-0.7.16a.tar.bz2 190773 BLAKE2B e1064381b6b1aa4c9b78d12222c7b783a55676a163b94ad8596a2af64c9b0d60bbebd8e840aaa13b25e1ca4f10466c2c39c99830f1ca58e558d724d1ad583944 SHA512 8bbe223f79efd328d66adb88baf995e894f5944aad912ac1b464dc84dc9b4e22ddf77b60dcbe468e0eedc344ee58d08dc498777f0d2794a2c1e0ddd33dad606d DIST bwa-0.7.17.tar.gz 232593 BLAKE2B fa48aad72a47547d66c767e2e2a5aadfcfc7c77c517410812230f51a2222ee66bb04383b068036b696af0a57b04b35e97bed11e3c44793aa899a8c0807f3df5e SHA512 114e61b7cc5edcb67172d1eca7be1fa670ea33dd48b5c02c98318e254871363775c0dab327fd7ee7023200a5fedc745fa01cbe0fd9550d783f091d4df6926f48 diff --git a/sci-biology/bwa/bwa-0.7.16a.ebuild b/sci-biology/bwa/bwa-0.7.16a.ebuild deleted file mode 100644 index b29bf210169..00000000000 --- a/sci-biology/bwa/bwa-0.7.16a.ebuild +++ /dev/null @@ -1,36 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit toolchain-funcs - -DESCRIPTION="Burrows-Wheeler Alignment Tool, a fast short genomic sequence aligner" -HOMEPAGE="https://bio-bwa.sourceforge.net/"; -SRC_URI="mirror://sourceforge/bio-bwa/${P}.tar.bz2" - -LICENSE="GPL-3" -SLOT="0" -KEYWORDS="~amd64 ~x86 ~x64-macos" - -RDEPEND="dev-lang/perl" - -PATCHES=( - "${FILESDIR}"/${PN}-0.7.15-Makefile.patch - "${FILESDIR}"/${PN}-0.7.16a-gcc-10.patch -) -DOCS=( NEWS.md README-alt.md README.md ) - -src_configure() { - tc-export CC AR -} - -src_install() { - dobin bwa - - exeinto /usr/libexec/${PN} - doexe qualfa2fq.pl xa2multi.pl - - einstalldocs - doman bwa.1 -} 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 39b437a0289..00000000000 --- 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/files/bwa-0.7.16a-gcc-10.patch b/sci-biology/bwa/files/bwa-0.7.16a-gcc-10.patch deleted file mode 100644 index 40056ffeaaa..00000000000 --- a/sci-biology/bwa/files/bwa-0.7.16a-gcc-10.patch +++ /dev/null @@ -1,7 +0,0 @@ ---- a/rle.h -+++ b/rle.h -@@ -32,3 +32,3 @@ extern "C" { - --const uint8_t rle_auxtab[8]; -+extern const uint8_t rle_auxtab[8]; -
