diff options
| author | V3n3RiX <venerix@redcorelinux.org> | 2017-10-09 18:53:29 +0100 |
|---|---|---|
| committer | V3n3RiX <venerix@redcorelinux.org> | 2017-10-09 18:53:29 +0100 |
| commit | 4f2d7949f03e1c198bc888f2d05f421d35c57e21 (patch) | |
| tree | ba5f07bf3f9d22d82e54a462313f5d244036c768 /sci-biology/bwa | |
reinit the tree, so we can have metadata
Diffstat (limited to 'sci-biology/bwa')
| -rw-r--r-- | sci-biology/bwa/Manifest | 6 | ||||
| -rw-r--r-- | sci-biology/bwa/bwa-0.7.16a.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, 78 insertions, 0 deletions
diff --git a/sci-biology/bwa/Manifest b/sci-biology/bwa/Manifest new file mode 100644 index 000000000000..266fd9dce775 --- /dev/null +++ b/sci-biology/bwa/Manifest @@ -0,0 +1,6 @@ +AUX bwa-0.7.15-Makefile.patch 933 SHA256 58b08ded78471266c0b7bfc6042bc52100b38c5c72a4091a1d9391ee9569ea5c SHA512 d76d6aac355b2ad52d3aa1ca59defc33017cfbdcec96939db4807acf7f35d6bcd4e21728998fb0fd3633742cfd9edaa7b62ab1eaff26829296967fefdbc185b4 WHIRLPOOL ab34cbed56aa60c940b5b4949eaed488ba0e01b24d43976e8706759e2f55bbd8a9a5c407571c9bfe08e3f443e7b1e099b9537d216cc4b1c4583ed5ce9c9499f3 +DIST bwa-0.7.16a.tar.bz2 190773 SHA256 8fecdb5f88871351bbe050c18d6078121456c36ad75c5c78f33a926560ffc170 SHA512 8bbe223f79efd328d66adb88baf995e894f5944aad912ac1b464dc84dc9b4e22ddf77b60dcbe468e0eedc344ee58d08dc498777f0d2794a2c1e0ddd33dad606d WHIRLPOOL 624d94bb65fcfdbefa709f8e873b29f11d940c0ee54fc627a3305641bb15548de1162241ece07341623dae3b9970a49a7377dd0e634454cfef59a9c357f8b3ec +EBUILD bwa-0.7.16a.ebuild 667 SHA256 9257024bd8d19bf602d21037480e90495573842a09e6261999f0f0fa46b044f4 SHA512 16abfaeabcec740ba001eb2c34c6bda6c464698319f7d206fad7b2b5905636885e51cac4eacaa4b4e6c80fcb38f50d6a78a8a06ab977e0632f0cc1b8fbef8632 WHIRLPOOL c673627bc361f9a887e725d5c678a9632fc49429b283952dcb8cb309e5657add27d134ac208d9acfad829f7d2291ade198b7aead6f98b1ddbf381cf881a21912 +MISC ChangeLog 2881 SHA256 df9a86f76fa853e1a6e1fb2c344553a8657846266c9af27e6a6717d2acd22125 SHA512 174470347e2b9dd3c2b5ae4dad6df6c1693a4d3debc8802f33383bb4b9e6a30c0fcd4a5e8ddf0921a0037a260e4e7828e4fa7586d640780e7b246dc5b81897a3 WHIRLPOOL 25113d6a569c17d901fa126621e69167ffbf1de424c7971236f1ff855fe7c0e6a7900d882524fb23edec972f1d5e071c27d35482221fda10c5a14bba11b83fab +MISC ChangeLog-2015 2597 SHA256 ea33c05fa080e2b98f2ceff38591e4a057b2214cdd58c04ba19daebe51d45343 SHA512 526bf2b02393e7b652fda2b64f5af2c2510da6ac4d88f846de4df6180e52f2894d3b4e940dda020caaa506ce5b6ee7f477117c8ab9348801b043ff21f4d078ef WHIRLPOOL 5076ca1b5a01dae4c891c652fff9ce91ab3ca4aea2a1df7a46853e4e9e0a48829ba38e745cc9aa3fe5b72ab96ef5623cc03bcc490e9b5cb1b3e8271140e05a6c +MISC metadata.xml 348 SHA256 be690c3df0f30980eec4b2d88b01cb640f8c7ece9e3ca70a68f15565edcd6349 SHA512 512439b23a870d55169998b035a6f9d8a10c0746c7e20d1f969a11a7b98eef297e71fc8fdf600a20f321e1f95a2c763d3e98ff4f089952eec38138ebf0291c6a WHIRLPOOL 8b164fe0e886f396d970c5fe68321d353a13eada641b9a4a9436b2f42d8f82ba5a51f9e12bf243fb47969d502b39fc172a8e9d4b5aa05f1066ff65e390419157 diff --git a/sci-biology/bwa/bwa-0.7.16a.ebuild b/sci-biology/bwa/bwa-0.7.16a.ebuild new file mode 100644 index 000000000000..21fe67143bd2 --- /dev/null +++ b/sci-biology/bwa/bwa-0.7.16a.ebuild @@ -0,0 +1,34 @@ +# 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="https://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 000000000000..39b437a02897 --- /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 000000000000..ceb43ead2a3f --- /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> |