| 1 |
commit: 7f516dcc0ff31783264d5aa43b598564d6dd5d1a |
| 2 |
Author: David Seifert <soap <AT> gentoo <DOT> org> |
| 3 |
AuthorDate: Sat Sep 2 08:11:47 2017 +0000 |
| 4 |
Commit: David Seifert <soap <AT> gentoo <DOT> org> |
| 5 |
CommitDate: Sat Sep 2 08:11:47 2017 +0000 |
| 6 |
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=7f516dcc |
| 7 |
|
| 8 |
sci-biology/bwa: Latest in main tree |
| 9 |
|
| 10 |
sci-biology/bwa/bwa-0.7.16.ebuild | 36 ------------------------- |
| 11 |
sci-biology/bwa/files/bwa-0.7.15-Makefile.patch | 27 ------------------- |
| 12 |
sci-biology/bwa/metadata.xml | 11 -------- |
| 13 |
3 files changed, 74 deletions(-) |
| 14 |
|
| 15 |
diff --git a/sci-biology/bwa/bwa-0.7.16.ebuild b/sci-biology/bwa/bwa-0.7.16.ebuild |
| 16 |
deleted file mode 100644 |
| 17 |
index 1568adff3..000000000 |
| 18 |
--- a/sci-biology/bwa/bwa-0.7.16.ebuild |
| 19 |
+++ /dev/null |
| 20 |
@@ -1,36 +0,0 @@ |
| 21 |
-# Copyright 1999-2017 Gentoo Foundation |
| 22 |
-# Distributed under the terms of the GNU General Public License v2 |
| 23 |
- |
| 24 |
-EAPI=6 |
| 25 |
- |
| 26 |
-inherit toolchain-funcs |
| 27 |
- |
| 28 |
-DESCRIPTION="Burrows-Wheeler Alignment Tool, a fast short genomic sequence aligner" |
| 29 |
-HOMEPAGE="http://bio-bwa.sourceforge.net/" |
| 30 |
-SRC_URI="mirror://sourceforge/bio-bwa/${P}.tar.bz2" |
| 31 |
- |
| 32 |
-LICENSE="GPL-3" |
| 33 |
-SLOT="0" |
| 34 |
-IUSE="" |
| 35 |
-KEYWORDS="~amd64 ~x86 ~x64-macos" |
| 36 |
- |
| 37 |
-RDEPEND="dev-lang/perl" |
| 38 |
- |
| 39 |
-DOCS=( NEWS.md README-alt.md README.md ) |
| 40 |
-PATCHES=( "${FILESDIR}"/${PN}-0.7.15-Makefile.patch ) |
| 41 |
- |
| 42 |
-src_configure() { |
| 43 |
- tc-export CC AR |
| 44 |
- default |
| 45 |
-} |
| 46 |
- |
| 47 |
-src_install() { |
| 48 |
- dobin bwa |
| 49 |
- |
| 50 |
- doman bwa.1 |
| 51 |
- |
| 52 |
- exeinto /usr/libexec/${PN} |
| 53 |
- doexe qualfa2fq.pl xa2multi.pl |
| 54 |
- |
| 55 |
- einstalldocs |
| 56 |
-} |
| 57 |
|
| 58 |
diff --git a/sci-biology/bwa/files/bwa-0.7.15-Makefile.patch b/sci-biology/bwa/files/bwa-0.7.15-Makefile.patch |
| 59 |
deleted file mode 100644 |
| 60 |
index 39b437a02..000000000 |
| 61 |
--- a/sci-biology/bwa/files/bwa-0.7.15-Makefile.patch |
| 62 |
+++ /dev/null |
| 63 |
@@ -1,27 +0,0 @@ |
| 64 |
---- bwa-0.7.13/Makefile |
| 65 |
-+++ bwa-0.7.13/Makefile |
| 66 |
-@@ -1,8 +1,8 @@ |
| 67 |
--CC= gcc |
| 68 |
-+CC?= gcc |
| 69 |
- #CC= clang --analyze |
| 70 |
--CFLAGS= -g -Wall -Wno-unused-function -O2 |
| 71 |
-+CFLAGS?= -g -Wall -Wno-unused-function -O2 |
| 72 |
- WRAP_MALLOC=-DUSE_MALLOC_WRAPPERS |
| 73 |
--AR= ar |
| 74 |
-+AR?= ar |
| 75 |
- DFLAGS= -DHAVE_PTHREAD $(WRAP_MALLOC) |
| 76 |
- LOBJS= utils.o kthread.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o bwamem_extra.o malloc_wrap.o |
| 77 |
- AOBJS= QSufSort.o bwt_gen.o bwashm.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o \ |
| 78 |
-@@ -26,10 +26,10 @@ |
| 79 |
- all:$(PROG) |
| 80 |
- |
| 81 |
- bwa:libbwa.a $(AOBJS) main.o |
| 82 |
-- $(CC) $(CFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS) |
| 83 |
-+ $(CC) $(CFLAGS) $(LDFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS) |
| 84 |
- |
| 85 |
- bwamem-lite:libbwa.a example.o |
| 86 |
-- $(CC) $(CFLAGS) $(DFLAGS) example.o -o $@ -L. -lbwa $(LIBS) |
| 87 |
-+ $(CC) $(CFLAGS) $(LDFLAGS) $(DFLAGS) example.o -o $@ -L. -lbwa $(LIBS) |
| 88 |
- |
| 89 |
- libbwa.a:$(LOBJS) |
| 90 |
- $(AR) -csru $@ $(LOBJS) |
| 91 |
|
| 92 |
diff --git a/sci-biology/bwa/metadata.xml b/sci-biology/bwa/metadata.xml |
| 93 |
deleted file mode 100644 |
| 94 |
index ceb43ead2..000000000 |
| 95 |
--- a/sci-biology/bwa/metadata.xml |
| 96 |
+++ /dev/null |
| 97 |
@@ -1,11 +0,0 @@ |
| 98 |
-<?xml version="1.0" encoding="UTF-8"?> |
| 99 |
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
| 100 |
-<pkgmetadata> |
| 101 |
- <maintainer type="project"> |
| 102 |
- <email>sci-biology@g.o</email> |
| 103 |
- <name>Gentoo Biology Project</name> |
| 104 |
- </maintainer> |
| 105 |
- <upstream> |
| 106 |
- <remote-id type="sourceforge">bio-bwa</remote-id> |
| 107 |
- </upstream> |
| 108 |
-</pkgmetadata> |
Archives