| 1 |
commit: 1a7c939f8f1087c8031e2621e53bd3bda0f043af |
| 2 |
Author: David Seifert <soap <AT> gentoo <DOT> org> |
| 3 |
AuthorDate: Sat Sep 26 10:00:48 2020 +0000 |
| 4 |
Commit: David Seifert <soap <AT> gentoo <DOT> org> |
| 5 |
CommitDate: Sat Sep 26 10:00:48 2020 +0000 |
| 6 |
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=1a7c939f |
| 7 |
|
| 8 |
sci-biology/bwa: Remove old 0.7.16a |
| 9 |
|
| 10 |
Package-Manager: Portage-3.0.8, Repoman-3.0.1 |
| 11 |
Signed-off-by: David Seifert <soap <AT> gentoo.org> |
| 12 |
|
| 13 |
sci-biology/bwa/Manifest | 1 - |
| 14 |
sci-biology/bwa/bwa-0.7.16a.ebuild | 36 ------------------------- |
| 15 |
sci-biology/bwa/files/bwa-0.7.15-Makefile.patch | 27 ------------------- |
| 16 |
sci-biology/bwa/files/bwa-0.7.16a-gcc-10.patch | 7 ----- |
| 17 |
4 files changed, 71 deletions(-) |
| 18 |
|
| 19 |
diff --git a/sci-biology/bwa/Manifest b/sci-biology/bwa/Manifest |
| 20 |
index 4b69e7f0403..5f912dc43cf 100644 |
| 21 |
--- a/sci-biology/bwa/Manifest |
| 22 |
+++ b/sci-biology/bwa/Manifest |
| 23 |
@@ -1,2 +1 @@ |
| 24 |
-DIST bwa-0.7.16a.tar.bz2 190773 BLAKE2B e1064381b6b1aa4c9b78d12222c7b783a55676a163b94ad8596a2af64c9b0d60bbebd8e840aaa13b25e1ca4f10466c2c39c99830f1ca58e558d724d1ad583944 SHA512 8bbe223f79efd328d66adb88baf995e894f5944aad912ac1b464dc84dc9b4e22ddf77b60dcbe468e0eedc344ee58d08dc498777f0d2794a2c1e0ddd33dad606d |
| 25 |
DIST bwa-0.7.17.tar.gz 232593 BLAKE2B fa48aad72a47547d66c767e2e2a5aadfcfc7c77c517410812230f51a2222ee66bb04383b068036b696af0a57b04b35e97bed11e3c44793aa899a8c0807f3df5e SHA512 114e61b7cc5edcb67172d1eca7be1fa670ea33dd48b5c02c98318e254871363775c0dab327fd7ee7023200a5fedc745fa01cbe0fd9550d783f091d4df6926f48 |
| 26 |
|
| 27 |
diff --git a/sci-biology/bwa/bwa-0.7.16a.ebuild b/sci-biology/bwa/bwa-0.7.16a.ebuild |
| 28 |
deleted file mode 100644 |
| 29 |
index b29bf210169..00000000000 |
| 30 |
--- a/sci-biology/bwa/bwa-0.7.16a.ebuild |
| 31 |
+++ /dev/null |
| 32 |
@@ -1,36 +0,0 @@ |
| 33 |
-# Copyright 1999-2020 Gentoo Authors |
| 34 |
-# Distributed under the terms of the GNU General Public License v2 |
| 35 |
- |
| 36 |
-EAPI=7 |
| 37 |
- |
| 38 |
-inherit toolchain-funcs |
| 39 |
- |
| 40 |
-DESCRIPTION="Burrows-Wheeler Alignment Tool, a fast short genomic sequence aligner" |
| 41 |
-HOMEPAGE="https://bio-bwa.sourceforge.net/" |
| 42 |
-SRC_URI="mirror://sourceforge/bio-bwa/${P}.tar.bz2" |
| 43 |
- |
| 44 |
-LICENSE="GPL-3" |
| 45 |
-SLOT="0" |
| 46 |
-KEYWORDS="~amd64 ~x86 ~x64-macos" |
| 47 |
- |
| 48 |
-RDEPEND="dev-lang/perl" |
| 49 |
- |
| 50 |
-PATCHES=( |
| 51 |
- "${FILESDIR}"/${PN}-0.7.15-Makefile.patch |
| 52 |
- "${FILESDIR}"/${PN}-0.7.16a-gcc-10.patch |
| 53 |
-) |
| 54 |
-DOCS=( NEWS.md README-alt.md README.md ) |
| 55 |
- |
| 56 |
-src_configure() { |
| 57 |
- tc-export CC AR |
| 58 |
-} |
| 59 |
- |
| 60 |
-src_install() { |
| 61 |
- dobin bwa |
| 62 |
- |
| 63 |
- exeinto /usr/libexec/${PN} |
| 64 |
- doexe qualfa2fq.pl xa2multi.pl |
| 65 |
- |
| 66 |
- einstalldocs |
| 67 |
- doman bwa.1 |
| 68 |
-} |
| 69 |
|
| 70 |
diff --git a/sci-biology/bwa/files/bwa-0.7.15-Makefile.patch b/sci-biology/bwa/files/bwa-0.7.15-Makefile.patch |
| 71 |
deleted file mode 100644 |
| 72 |
index 39b437a0289..00000000000 |
| 73 |
--- a/sci-biology/bwa/files/bwa-0.7.15-Makefile.patch |
| 74 |
+++ /dev/null |
| 75 |
@@ -1,27 +0,0 @@ |
| 76 |
---- bwa-0.7.13/Makefile |
| 77 |
-+++ bwa-0.7.13/Makefile |
| 78 |
-@@ -1,8 +1,8 @@ |
| 79 |
--CC= gcc |
| 80 |
-+CC?= gcc |
| 81 |
- #CC= clang --analyze |
| 82 |
--CFLAGS= -g -Wall -Wno-unused-function -O2 |
| 83 |
-+CFLAGS?= -g -Wall -Wno-unused-function -O2 |
| 84 |
- WRAP_MALLOC=-DUSE_MALLOC_WRAPPERS |
| 85 |
--AR= ar |
| 86 |
-+AR?= ar |
| 87 |
- DFLAGS= -DHAVE_PTHREAD $(WRAP_MALLOC) |
| 88 |
- LOBJS= utils.o kthread.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o bwamem_extra.o malloc_wrap.o |
| 89 |
- AOBJS= QSufSort.o bwt_gen.o bwashm.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o \ |
| 90 |
-@@ -26,10 +26,10 @@ |
| 91 |
- all:$(PROG) |
| 92 |
- |
| 93 |
- bwa:libbwa.a $(AOBJS) main.o |
| 94 |
-- $(CC) $(CFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS) |
| 95 |
-+ $(CC) $(CFLAGS) $(LDFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS) |
| 96 |
- |
| 97 |
- bwamem-lite:libbwa.a example.o |
| 98 |
-- $(CC) $(CFLAGS) $(DFLAGS) example.o -o $@ -L. -lbwa $(LIBS) |
| 99 |
-+ $(CC) $(CFLAGS) $(LDFLAGS) $(DFLAGS) example.o -o $@ -L. -lbwa $(LIBS) |
| 100 |
- |
| 101 |
- libbwa.a:$(LOBJS) |
| 102 |
- $(AR) -csru $@ $(LOBJS) |
| 103 |
|
| 104 |
diff --git a/sci-biology/bwa/files/bwa-0.7.16a-gcc-10.patch b/sci-biology/bwa/files/bwa-0.7.16a-gcc-10.patch |
| 105 |
deleted file mode 100644 |
| 106 |
index 40056ffeaaa..00000000000 |
| 107 |
--- a/sci-biology/bwa/files/bwa-0.7.16a-gcc-10.patch |
| 108 |
+++ /dev/null |
| 109 |
@@ -1,7 +0,0 @@ |
| 110 |
---- a/rle.h |
| 111 |
-+++ b/rle.h |
| 112 |
-@@ -32,3 +32,3 @@ extern "C" { |
| 113 |
- |
| 114 |
--const uint8_t rle_auxtab[8]; |
| 115 |
-+extern const uint8_t rle_auxtab[8]; |
| 116 |
- |
Archives