commit: cec8859662ffa14fd17eeb93abd6e9aeb0a088a6 Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Sun Jun 24 08:28:22 2018 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Sun Jun 24 08:28:22 2018 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=cec88596
sci-biology/bwa: version bump Also fix HOMEPAGE which does not listen on https (anymore?) Package-Manager: Portage-2.3.40, Repoman-2.3.9 sci-biology/bwa/bwa-0.7.17.ebuild | 34 +++++++++++++++++++++++++ sci-biology/bwa/files/bwa-0.7.15-Makefile.patch | 27 ++++++++++++++++++++ sci-biology/bwa/metadata.xml | 11 ++++++++ 3 files changed, 72 insertions(+) diff --git a/sci-biology/bwa/bwa-0.7.17.ebuild b/sci-biology/bwa/bwa-0.7.17.ebuild new file mode 100644 index 000000000..429ba43e6 --- /dev/null +++ b/sci-biology/bwa/bwa-0.7.17.ebuild @@ -0,0 +1,34 @@ +# Copyright 1999-2018 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/${P}.tar.bz2" + +LICENSE="GPL-3" +SLOT="0" +IUSE="" +KEYWORDS="~amd64 ~x86 ~x64-macos" + +RDEPEND="dev-lang/perl" + +PATCHES=( "${FILESDIR}"/${PN}-0.7.15-Makefile.patch ) +DOCS=( NEWS.md README-alt.md README.md ) + +src_configure() { + tc-export CC AR +} + +src_install() { + dobin bwa + + exeinto /usr/libexec/${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 new file mode 100644 index 000000000..39b437a02 --- /dev/null +++ b/sci-biology/bwa/files/bwa-0.7.15-Makefile.patch @@ -0,0 +1,27 @@ +--- 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 new file mode 100644 index 000000000..ceb43ead2 --- /dev/null +++ b/sci-biology/bwa/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> +<pkgmetadata> + <maintainer type="project"> + <email>[email protected]</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">bio-bwa</remote-id> + </upstream> +</pkgmetadata>
