diff options
| -rw-r--r-- | sci-biology/bwa/Manifest | 1 | ||||
| -rw-r--r-- | sci-biology/bwa/bwa-0.7.17.ebuild | 34 | ||||
| -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, 73 insertions, 0 deletions
diff --git a/sci-biology/bwa/Manifest b/sci-biology/bwa/Manifest new file mode 100644 index 000000000..d5ec96afa --- /dev/null +++ b/sci-biology/bwa/Manifest @@ -0,0 +1 @@ +DIST bwa-0.7.17.tar.bz2 190908 BLAKE2B d646352719a692d35d39ffcfbdbfdbda5d431f3b89b0d8dbc6abc21b64b249512322b123c95190ad35b65fbf3185ba86e8530d060c222d4b3a1787d338779419 SHA512 67cccfef1c7aa1b5aad6b59a49390e8d96f64320c414bfffacf232aeb08c15861e98be826c1b42b6222d6ff086eeb055b1318ea2e9eebfd87b2365d06fc89802 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>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">bio-bwa</remote-id> + </upstream> +</pkgmetadata> |