aboutsummaryrefslogtreecommitdiff
diff options
context:
space:
mode:
authorDavid Seifert <soap@gentoo.org>2016-05-08 01:20:43 +0200
committerDavid Seifert <soap@gentoo.org>2016-05-08 01:20:43 +0200
commit1af3cb1d79a54e814b222cb56e4de3630136b828 (patch)
tree245e32ad67080031bd909dc246ee4327fd56d155 /sci-biology/bwa
parentDrop invalid deps (diff)
downloadsci-1af3cb1d79a54e814b222cb56e4de3630136b828.tar.gz
sci-1af3cb1d79a54e814b222cb56e4de3630136b828.tar.bz2
sci-1af3cb1d79a54e814b222cb56e4de3630136b828.zip
sci-biology/bwa: move to main tree
Diffstat (limited to 'sci-biology/bwa')
-rw-r--r--sci-biology/bwa/Manifest1
-rw-r--r--sci-biology/bwa/bwa-0.7.13.ebuild36
-rw-r--r--sci-biology/bwa/files/bwa-0.7.13-Makefile.patch27
-rw-r--r--sci-biology/bwa/metadata.xml11
4 files changed, 0 insertions, 75 deletions
diff --git a/sci-biology/bwa/Manifest b/sci-biology/bwa/Manifest
deleted file mode 100644
index 5e46094ed..000000000
--- a/sci-biology/bwa/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST bwa-0.7.13.tar.bz2 189670 SHA256 559b3c63266e5d5351f7665268263dbb9592f3c1c4569e7a4a75a15f17f0aedc SHA512 37966e914321d17b5a1d4e3a7786abdd9dd476e4dd7aaf924fb0e0726e3827a1414d9ffccc114a1a334943c8dde38273ce5fafdd1b429ab0f3cbf47ddbd6bedf WHIRLPOOL 86b278b301aa1ff4334c0d78709a61dc034895deb6aa2bd60ee45a595198343e7d60db458c61168b8c61a6ace21db394583b6314a56df3171a151f554c07f769
diff --git a/sci-biology/bwa/bwa-0.7.13.ebuild b/sci-biology/bwa/bwa-0.7.13.ebuild
deleted file mode 100644
index 27f314b7b..000000000
--- a/sci-biology/bwa/bwa-0.7.13.ebuild
+++ /dev/null
@@ -1,36 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-inherit eutils 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/${P}.tar.bz2"
-
-LICENSE="GPL-3"
-# bwa-0.7.13 has "Apache2" branch with Apache2-licensed BWA with ropebwt2 index
-# feature which is slower than "bwtsw" algorithm but it has a permissive license.
-SLOT="0"
-IUSE=""
-KEYWORDS="~amd64 ~x86 ~x64-macos"
-
-PATCHES=( "${FILESDIR}"/${P}-Makefile.patch )
-
-src_prepare() {
- epatch ${PATCHES[@]}
- tc-export CC AR
-}
-
-src_install() {
- dobin bwa
-
- doman bwa.1
-
- exeinto /usr/libexec/${PN}
- doexe qualfa2fq.pl xa2multi.pl
-
- dodoc NEWS.md README-alt.md README.md
-}
diff --git a/sci-biology/bwa/files/bwa-0.7.13-Makefile.patch b/sci-biology/bwa/files/bwa-0.7.13-Makefile.patch
deleted file mode 100644
index 406e9b052..000000000
--- a/sci-biology/bwa/files/bwa-0.7.13-Makefile.patch
+++ /dev/null
@@ -1,27 +0,0 @@
---- Makefile
-+++ 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>