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authorDavid Seifert <soap@gentoo.org>2017-09-02 10:11:47 +0200
committerDavid Seifert <soap@gentoo.org>2017-09-02 10:11:47 +0200
commit7f516dcc0ff31783264d5aa43b598564d6dd5d1a (patch)
treed571fc53cde11c73c1de3f55979914ddaca9a382
parentnumeric-int64-multibuild.eclass: consider _static build variant. (diff)
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sci-biology/bwa: Latest in main tree
-rw-r--r--sci-biology/bwa/Manifest1
-rw-r--r--sci-biology/bwa/bwa-0.7.16.ebuild36
-rw-r--r--sci-biology/bwa/files/bwa-0.7.15-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 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>