[gentoo-commits] proj/sci:master commit in: sci-biology/bwa/, sci-biology/bwa/files/

["David Seifert" <soap@gentoo.org>]

commit:     7f516dcc0ff31783264d5aa43b598564d6dd5d1a
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sat Sep  2 08:11:47 2017 +0000
Commit:     David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sat Sep  2 08:11:47 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=7f516dcc

sci-biology/bwa: Latest in main tree

 sci-biology/bwa/bwa-0.7.16.ebuild               | 36 -------------------------
 sci-biology/bwa/files/bwa-0.7.15-Makefile.patch | 27 -------------------
 sci-biology/bwa/metadata.xml                    | 11 --------
 3 files changed, 74 deletions(-)

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>