* [gentoo-commits] proj/sci:master commit in: sci-biology/bwa/files/, sci-biology/bwa/
@ 2015-03-03 15:17 git@oystercatcher mirror+tproxy
0 siblings, 0 replies; 4+ messages in thread
From: git@oystercatcher mirror+tproxy @ 2015-03-03 15:17 UTC (permalink / raw
To: gentoo-commits
commit: de8eb4ef90bedc116258edad0d769d7469dbc28c
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Mar 3 15:16:58 2015 +0000
Commit: git@oystercatcher mirror+tproxy <git <AT> oystercatcher <DOT> gentoo <DOT> org>
CommitDate: Tue Mar 3 15:16:58 2015 +0000
URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=de8eb4ef
IMport to CVS
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
sci-biology/bwa/bwa-0.7.12.ebuild | 34 --------------------------------
sci-biology/bwa/files/bwa_Makefile.patch | 27 -------------------------
sci-biology/bwa/metadata.xml | 5 -----
3 files changed, 66 deletions(-)
diff --git a/sci-biology/bwa/bwa-0.7.12.ebuild b/sci-biology/bwa/bwa-0.7.12.ebuild
deleted file mode 100644
index 62488f3..0000000
--- a/sci-biology/bwa/bwa-0.7.12.ebuild
+++ /dev/null
@@ -1,34 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-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/${P}.tar.bz2"
-
-LICENSE="GPL-3"
-SLOT="0"
-IUSE=""
-KEYWORDS="~amd64 ~x86 ~x64-macos"
-
-PATCHES=( "${FILESDIR}"/${PN}_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_Makefile.patch b/sci-biology/bwa/files/bwa_Makefile.patch
deleted file mode 100644
index 406e9b0..0000000
--- a/sci-biology/bwa/files/bwa_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 f17a827..0000000
--- a/sci-biology/bwa/metadata.xml
+++ /dev/null
@@ -1,5 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <herd>sci-biology</herd>
-</pkgmetadata>
^ permalink raw reply related [flat|nested] 4+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/bwa/files/, sci-biology/bwa/
@ 2016-05-17 9:19 Marius Brehler
0 siblings, 0 replies; 4+ messages in thread
From: Marius Brehler @ 2016-05-17 9:19 UTC (permalink / raw
To: gentoo-commits
commit: 1af3cb1d79a54e814b222cb56e4de3630136b828
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sat May 7 23:20:43 2016 +0000
Commit: Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
CommitDate: Sat May 7 23:20:43 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=1af3cb1d
sci-biology/bwa: move to main tree
sci-biology/bwa/bwa-0.7.13.ebuild | 36 -------------------------
sci-biology/bwa/files/bwa-0.7.13-Makefile.patch | 27 -------------------
sci-biology/bwa/metadata.xml | 11 --------
3 files changed, 74 deletions(-)
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 27f314b..0000000
--- 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 406e9b0..0000000
--- 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 ceb43ea..0000000
--- 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>
^ permalink raw reply related [flat|nested] 4+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/bwa/files/, sci-biology/bwa/
@ 2017-07-31 11:26 Martin Mokrejs
0 siblings, 0 replies; 4+ messages in thread
From: Martin Mokrejs @ 2017-07-31 11:26 UTC (permalink / raw
To: gentoo-commits
commit: ca813e4a288c12c2fee6734cd97c73e86e129920
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Jul 31 11:25:53 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Jul 31 11:25:53 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=ca813e4a
sci-biology/bwa: version bump
Release 0.7.16 (30 July 2017)
-----------------------------
This release added a couple of minor features and incorporated multiple pull
requests, including:
* Added option -5, which is useful to some Hi-C pipelines.
* Fixed an error with samtools sorting (#129). Updated download link for
GRCh38 (#123). Fixed README MarkDown formatting (#70). Addressed multiple
issues via a collected pull request #139 by @jmarshall. Avoid malformatted
SAM header when -R is used with TAB (#84). Output mate CIGAR (#138).
This release is expected to give the same alignment as 0.7.15, except the added
mate-cigar tag.
(0.7.16: 30 July 2017, r1180)
https://lists.sourceforge.net/lists/listinfo/bio-bwa-help
Package-Manager: Portage-2.3.6, Repoman-2.3.3
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 insertions(+)
diff --git a/sci-biology/bwa/bwa-0.7.16.ebuild b/sci-biology/bwa/bwa-0.7.16.ebuild
new file mode 100644
index 000000000..1568adff3
--- /dev/null
+++ b/sci-biology/bwa/bwa-0.7.16.ebuild
@@ -0,0 +1,36 @@
+# 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
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>
^ permalink raw reply related [flat|nested] 4+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/bwa/files/, sci-biology/bwa/
@ 2018-06-24 8:28 Martin Mokrejs
0 siblings, 0 replies; 4+ messages in thread
From: Martin Mokrejs @ 2018-06-24 8:28 UTC (permalink / raw
To: gentoo-commits
commit: cec8859662ffa14fd17eeb93abd6e9aeb0a088a6
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Jun 24 08:28:22 2018 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Jun 24 08:28:22 2018 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=cec88596
sci-biology/bwa: version bump
Also fix HOMEPAGE which does not listen on https (anymore?)
Package-Manager: Portage-2.3.40, Repoman-2.3.9
sci-biology/bwa/bwa-0.7.17.ebuild | 34 +++++++++++++++++++++++++
sci-biology/bwa/files/bwa-0.7.15-Makefile.patch | 27 ++++++++++++++++++++
sci-biology/bwa/metadata.xml | 11 ++++++++
3 files changed, 72 insertions(+)
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>
^ permalink raw reply related [flat|nested] 4+ messages in thread
end of thread, other threads:[~2018-06-24 8:28 UTC | newest]
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2015-03-03 15:17 git@oystercatcher mirror+tproxy
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