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| author |   David Seifert <soap@gentoo.org> | 2017-09-02 10:11:47 +0200 |
|---|---|---|
| committer | David Seifert <soap@gentoo.org> | 2017-09-02 10:11:47 +0200 |
| commit | 7f516dcc0ff31783264d5aa43b598564d6dd5d1a (patch) | |
| tree | d571fc53cde11c73c1de3f55979914ddaca9a382 | |
| parent | numeric-int64-multibuild.eclass: consider _static build variant. (diff) | |
| download | sci-7f516dcc.tar.gz sci-7f516dcc.tar.bz2 sci-7f516dcc.zip | |
sci-biology/bwa: Latest in main tree
| -rw-r--r-- | sci-biology/bwa/Manifest | 1 | ||||
| -rw-r--r-- | sci-biology/bwa/bwa-0.7.16.ebuild | 36 | ||||
| -rw-r--r-- | sci-biology/bwa/files/bwa-0.7.15-Makefile.patch | 27 | ||||
| -rw-r--r-- | sci-biology/bwa/metadata.xml | 11 |
4 files changed, 0 insertions, 75 deletions
diff --git a/sci-biology/bwa/Manifest b/sci-biology/bwa/Manifest deleted file mode 100644 index b46b6d946..000000000 --- a/sci-biology/bwa/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST bwa-0.7.16.tar.bz2 191915 SHA256 4b7da7991b9fc105bea5ef37a1db77cdf91f8039b623182627316f896e008cd4 SHA512 50ae72298dc8e450a4f9d5a337d4f3e510625d02f92b570d908db04161e4cbdd22759220b519cb6b6fd73d205e92346ef2d6ed857a4797a978d3709010637000 WHIRLPOOL 66961ce29afd7d642e32a651373a6425c2917844dfd9a2d9b972546e64c5dfe232193809c03cbd6d3686c8a11c712b4c5054fc669c98fbc0e0a4a7a6069ccaba 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-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="sourceforge">bio-bwa</remote-id> - </upstream> -</pkgmetadata> |