* [gentoo-commits] repo/gentoo:master commit in: sci-biology/bwa/files/, sci-biology/bwa/
@ 2016-05-07 23:18 David Seifert
0 siblings, 0 replies; 5+ messages in thread
From: David Seifert @ 2016-05-07 23:18 UTC (permalink / raw
To: gentoo-commits
commit: c1fb3811426183133b6ee50bc58f03f2a90e93ca
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sat May 7 23:17:41 2016 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sat May 7 23:17:54 2016 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=c1fb3811
sci-biology/bwa: Version bump
Package-Manager: portage-2.2.28
sci-biology/bwa/Manifest | 1 +
sci-biology/bwa/bwa-0.7.13.ebuild | 38 +++++++++++++++++++++++++
sci-biology/bwa/files/bwa-0.7.13-Makefile.patch | 27 ++++++++++++++++++
3 files changed, 66 insertions(+)
diff --git a/sci-biology/bwa/Manifest b/sci-biology/bwa/Manifest
index 9c0d995..3cf0fb1 100644
--- a/sci-biology/bwa/Manifest
+++ b/sci-biology/bwa/Manifest
@@ -1 +1,2 @@
DIST bwa-0.7.12.tar.bz2 184599 SHA256 701dcad147ae470d741717a72c369b338df7f80bff4bb8eee8176c66f16d608c SHA512 3ea093b861c1596d20b1ee0336468b66e52bc9f26e3d0bcbba0ddccc7fe9b1af2c7e1ed2a4e1366fe93fec348152becc126d5f4685dae54f05e6c582488b3abd WHIRLPOOL 4b8651dedf2e09980850e7212fc2a77dc86b06f708af2077cff28cc843858b15825a203e3e02e7728418e9eb539004404f7c4b234c1f65de6a7b7dfe4dcfd1d0
+DIST bwa-0.7.13.tar.bz2 189670 SHA256 559b3c63266e5d5351f7665268263dbb9592f3c1c4569e7a4a75a15f17f0aedc SHA512 37966e914321d17b5a1d4e3a7786abdd9dd476e4dd7aaf924fb0e0726e3827a1414d9ffccc114a1a334943c8dde38273ce5fafdd1b429ab0f3cbf47ddbd6bedf WHIRLPOOL 86b278b301aa1ff4334c0d78709a61dc034895deb6aa2bd60ee45a595198343e7d60db458c61168b8c61a6ace21db394583b6314a56df3171a151f554c07f769
diff --git a/sci-biology/bwa/bwa-0.7.13.ebuild b/sci-biology/bwa/bwa-0.7.13.ebuild
new file mode 100644
index 0000000..2ce3ff3
--- /dev/null
+++ b/sci-biology/bwa/bwa-0.7.13.ebuild
@@ -0,0 +1,38 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+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}"/${P}-Makefile.patch
+)
+
+src_prepare() {
+ default
+ tc-export CC AR
+}
+
+src_install() {
+ dobin bwa
+
+ doman bwa.1
+
+ exeinto /usr/libexec/${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
new file mode 100644
index 0000000..39b437a
--- /dev/null
+++ b/sci-biology/bwa/files/bwa-0.7.13-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)
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/bwa/files/, sci-biology/bwa/
@ 2016-09-03 8:56 David Seifert
0 siblings, 0 replies; 5+ messages in thread
From: David Seifert @ 2016-09-03 8:56 UTC (permalink / raw
To: gentoo-commits
commit: 9574df41e529782826a9e6b32bdbac1678f47875
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sat Sep 3 08:55:18 2016 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sat Sep 3 08:55:18 2016 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=9574df41
sci-biology/bwa: Version bump to 0.7.15
Package-Manager: portage-2.3.0
sci-biology/bwa/Manifest | 2 +-
sci-biology/bwa/{bwa-0.7.13.ebuild => bwa-0.7.15.ebuild} | 11 +++++------
.../{bwa-0.7.13-Makefile.patch => bwa-0.7.15-Makefile.patch} | 0
3 files changed, 6 insertions(+), 7 deletions(-)
diff --git a/sci-biology/bwa/Manifest b/sci-biology/bwa/Manifest
index 3cf0fb1..5589b91 100644
--- a/sci-biology/bwa/Manifest
+++ b/sci-biology/bwa/Manifest
@@ -1,2 +1,2 @@
DIST bwa-0.7.12.tar.bz2 184599 SHA256 701dcad147ae470d741717a72c369b338df7f80bff4bb8eee8176c66f16d608c SHA512 3ea093b861c1596d20b1ee0336468b66e52bc9f26e3d0bcbba0ddccc7fe9b1af2c7e1ed2a4e1366fe93fec348152becc126d5f4685dae54f05e6c582488b3abd WHIRLPOOL 4b8651dedf2e09980850e7212fc2a77dc86b06f708af2077cff28cc843858b15825a203e3e02e7728418e9eb539004404f7c4b234c1f65de6a7b7dfe4dcfd1d0
-DIST bwa-0.7.13.tar.bz2 189670 SHA256 559b3c63266e5d5351f7665268263dbb9592f3c1c4569e7a4a75a15f17f0aedc SHA512 37966e914321d17b5a1d4e3a7786abdd9dd476e4dd7aaf924fb0e0726e3827a1414d9ffccc114a1a334943c8dde38273ce5fafdd1b429ab0f3cbf47ddbd6bedf WHIRLPOOL 86b278b301aa1ff4334c0d78709a61dc034895deb6aa2bd60ee45a595198343e7d60db458c61168b8c61a6ace21db394583b6314a56df3171a151f554c07f769
+DIST bwa-0.7.15.tar.bz2 189806 SHA256 2f56afefa49acc9bf45f12edb58e412565086cc20be098b8bf15ec07de8c0515 SHA512 cb862342aef1042751de55df095b4dac8344d9b41f00b0cca7f748829bf7fba71d15e4c7deaaa255eca6ee6af3ba58b370944ee702150cf17c29fb50ff25fa26 WHIRLPOOL 5d57d37339ff6c68c47ba0147ea21e4faa9a6cbbea2e66130e69bbb19802621ad22ae26889c06000109684961ed9d872605bffd469ddf97af2f1fdca3b8bd316
diff --git a/sci-biology/bwa/bwa-0.7.13.ebuild b/sci-biology/bwa/bwa-0.7.15.ebuild
similarity index 82%
rename from sci-biology/bwa/bwa-0.7.13.ebuild
rename to sci-biology/bwa/bwa-0.7.15.ebuild
index 2ce3ff3..fab85aa 100644
--- a/sci-biology/bwa/bwa-0.7.13.ebuild
+++ b/sci-biology/bwa/bwa-0.7.15.ebuild
@@ -17,13 +17,12 @@ KEYWORDS="~amd64 ~x86 ~x64-macos"
RDEPEND="dev-lang/perl"
-PATCHES=(
- "${FILESDIR}"/${P}-Makefile.patch
-)
+DOCS=( NEWS.md README-alt.md README.md )
+PATCHES=( "${FILESDIR}"/${P}-Makefile.patch )
-src_prepare() {
- default
+src_configure() {
tc-export CC AR
+ default
}
src_install() {
@@ -34,5 +33,5 @@ src_install() {
exeinto /usr/libexec/${PN}
doexe qualfa2fq.pl xa2multi.pl
- dodoc NEWS.md README-alt.md README.md
+ einstalldocs
}
diff --git a/sci-biology/bwa/files/bwa-0.7.13-Makefile.patch b/sci-biology/bwa/files/bwa-0.7.15-Makefile.patch
similarity index 100%
rename from sci-biology/bwa/files/bwa-0.7.13-Makefile.patch
rename to sci-biology/bwa/files/bwa-0.7.15-Makefile.patch
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/bwa/files/, sci-biology/bwa/
@ 2017-09-02 12:37 David Seifert
0 siblings, 0 replies; 5+ messages in thread
From: David Seifert @ 2017-09-02 12:37 UTC (permalink / raw
To: gentoo-commits
commit: 59716472229d52eacd4bba26ac2d90a9b3f44233
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sat Sep 2 11:07:41 2017 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sat Sep 2 12:36:56 2017 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=59716472
sci-biology/bwa: Remove old
Package-Manager: Portage-2.3.8, Repoman-2.3.3
Closes: https://github.com/gentoo/gentoo/pull/5593
sci-biology/bwa/Manifest | 2 --
sci-biology/bwa/bwa-0.7.12.ebuild | 33 -----------------------
sci-biology/bwa/bwa-0.7.15.ebuild | 36 -------------------------
sci-biology/bwa/files/bwa-0.7.12-Makefile.patch | 27 -------------------
4 files changed, 98 deletions(-)
diff --git a/sci-biology/bwa/Manifest b/sci-biology/bwa/Manifest
index d2daff2272e..e555b974c77 100644
--- a/sci-biology/bwa/Manifest
+++ b/sci-biology/bwa/Manifest
@@ -1,3 +1 @@
-DIST bwa-0.7.12.tar.bz2 184599 SHA256 701dcad147ae470d741717a72c369b338df7f80bff4bb8eee8176c66f16d608c SHA512 3ea093b861c1596d20b1ee0336468b66e52bc9f26e3d0bcbba0ddccc7fe9b1af2c7e1ed2a4e1366fe93fec348152becc126d5f4685dae54f05e6c582488b3abd WHIRLPOOL 4b8651dedf2e09980850e7212fc2a77dc86b06f708af2077cff28cc843858b15825a203e3e02e7728418e9eb539004404f7c4b234c1f65de6a7b7dfe4dcfd1d0
-DIST bwa-0.7.15.tar.bz2 189806 SHA256 2f56afefa49acc9bf45f12edb58e412565086cc20be098b8bf15ec07de8c0515 SHA512 cb862342aef1042751de55df095b4dac8344d9b41f00b0cca7f748829bf7fba71d15e4c7deaaa255eca6ee6af3ba58b370944ee702150cf17c29fb50ff25fa26 WHIRLPOOL 5d57d37339ff6c68c47ba0147ea21e4faa9a6cbbea2e66130e69bbb19802621ad22ae26889c06000109684961ed9d872605bffd469ddf97af2f1fdca3b8bd316
DIST bwa-0.7.16a.tar.bz2 190773 SHA256 8fecdb5f88871351bbe050c18d6078121456c36ad75c5c78f33a926560ffc170 SHA512 8bbe223f79efd328d66adb88baf995e894f5944aad912ac1b464dc84dc9b4e22ddf77b60dcbe468e0eedc344ee58d08dc498777f0d2794a2c1e0ddd33dad606d WHIRLPOOL 624d94bb65fcfdbefa709f8e873b29f11d940c0ee54fc627a3305641bb15548de1162241ece07341623dae3b9970a49a7377dd0e634454cfef59a9c357f8b3ec
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 86f3d3e86c4..00000000000
--- a/sci-biology/bwa/bwa-0.7.12.ebuild
+++ /dev/null
@@ -1,33 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-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}"/${P}-Makefile.patch )
-
-src_prepare() {
- epatch "${PATCHES[@]}"
- tc-export CC AR
-}
-
-src_install() {
- dobin bwa
-
- doman bwa.1
-
- exeinto /usr/libexec/${PN}
- doexe qualfa2fq.pl xa2multi.pl
-
- dodoc NEWS.md README-alt.md README.md
-}
diff --git a/sci-biology/bwa/bwa-0.7.15.ebuild b/sci-biology/bwa/bwa-0.7.15.ebuild
deleted file mode 100644
index 0c8b90d357e..00000000000
--- a/sci-biology/bwa/bwa-0.7.15.ebuild
+++ /dev/null
@@ -1,36 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit toolchain-funcs
-
-DESCRIPTION="Burrows-Wheeler Alignment Tool, a fast short genomic sequence aligner"
-HOMEPAGE="http://bio-bwa.sourceforge.net/"
-SRC_URI="mirror://sourceforge/bio-bwa/${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=( "${FILESDIR}"/${P}-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-0.7.12-Makefile.patch b/sci-biology/bwa/files/bwa-0.7.12-Makefile.patch
deleted file mode 100644
index 406e9b05237..00000000000
--- a/sci-biology/bwa/files/bwa-0.7.12-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 $@ $(LOBJS)
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/bwa/files/, sci-biology/bwa/
@ 2020-01-25 19:38 David Seifert
0 siblings, 0 replies; 5+ messages in thread
From: David Seifert @ 2020-01-25 19:38 UTC (permalink / raw
To: gentoo-commits
commit: 71f83be9beeb1ed4c39d0e0ad442a8aba54a2c8c
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sat Jan 25 19:38:35 2020 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sat Jan 25 19:38:35 2020 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=71f83be9
sci-biology/bwa: Fix -fno-common bug
Closes: https://bugs.gentoo.org/706348
Package-Manager: Portage-2.3.85, Repoman-2.3.20
Signed-off-by: David Seifert <soap <AT> gentoo.org>
sci-biology/bwa/bwa-0.7.16a.ebuild | 10 ++++++----
sci-biology/bwa/files/bwa-0.7.16a-gcc-10.patch | 7 +++++++
2 files changed, 13 insertions(+), 4 deletions(-)
diff --git a/sci-biology/bwa/bwa-0.7.16a.ebuild b/sci-biology/bwa/bwa-0.7.16a.ebuild
index 21fe67143bd..b29bf210169 100644
--- a/sci-biology/bwa/bwa-0.7.16a.ebuild
+++ b/sci-biology/bwa/bwa-0.7.16a.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2020 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=6
+EAPI=7
inherit toolchain-funcs
@@ -11,12 +11,14 @@ SRC_URI="mirror://sourceforge/bio-bwa/${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 )
+PATCHES=(
+ "${FILESDIR}"/${PN}-0.7.15-Makefile.patch
+ "${FILESDIR}"/${PN}-0.7.16a-gcc-10.patch
+)
DOCS=( NEWS.md README-alt.md README.md )
src_configure() {
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
new file mode 100644
index 00000000000..40056ffeaaa
--- /dev/null
+++ b/sci-biology/bwa/files/bwa-0.7.16a-gcc-10.patch
@@ -0,0 +1,7 @@
+--- a/rle.h
++++ b/rle.h
+@@ -32,3 +32,3 @@ extern "C" {
+
+-const uint8_t rle_auxtab[8];
++extern const uint8_t rle_auxtab[8];
+
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/bwa/files/, sci-biology/bwa/
@ 2020-09-26 10:01 David Seifert
0 siblings, 0 replies; 5+ messages in thread
From: David Seifert @ 2020-09-26 10:01 UTC (permalink / raw
To: gentoo-commits
commit: 1a7c939f8f1087c8031e2621e53bd3bda0f043af
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sat Sep 26 10:00:48 2020 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sat Sep 26 10:00:48 2020 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=1a7c939f
sci-biology/bwa: Remove old 0.7.16a
Package-Manager: Portage-3.0.8, Repoman-3.0.1
Signed-off-by: David Seifert <soap <AT> gentoo.org>
sci-biology/bwa/Manifest | 1 -
sci-biology/bwa/bwa-0.7.16a.ebuild | 36 -------------------------
sci-biology/bwa/files/bwa-0.7.15-Makefile.patch | 27 -------------------
sci-biology/bwa/files/bwa-0.7.16a-gcc-10.patch | 7 -----
4 files changed, 71 deletions(-)
diff --git a/sci-biology/bwa/Manifest b/sci-biology/bwa/Manifest
index 4b69e7f0403..5f912dc43cf 100644
--- a/sci-biology/bwa/Manifest
+++ b/sci-biology/bwa/Manifest
@@ -1,2 +1 @@
-DIST bwa-0.7.16a.tar.bz2 190773 BLAKE2B e1064381b6b1aa4c9b78d12222c7b783a55676a163b94ad8596a2af64c9b0d60bbebd8e840aaa13b25e1ca4f10466c2c39c99830f1ca58e558d724d1ad583944 SHA512 8bbe223f79efd328d66adb88baf995e894f5944aad912ac1b464dc84dc9b4e22ddf77b60dcbe468e0eedc344ee58d08dc498777f0d2794a2c1e0ddd33dad606d
DIST bwa-0.7.17.tar.gz 232593 BLAKE2B fa48aad72a47547d66c767e2e2a5aadfcfc7c77c517410812230f51a2222ee66bb04383b068036b696af0a57b04b35e97bed11e3c44793aa899a8c0807f3df5e SHA512 114e61b7cc5edcb67172d1eca7be1fa670ea33dd48b5c02c98318e254871363775c0dab327fd7ee7023200a5fedc745fa01cbe0fd9550d783f091d4df6926f48
diff --git a/sci-biology/bwa/bwa-0.7.16a.ebuild b/sci-biology/bwa/bwa-0.7.16a.ebuild
deleted file mode 100644
index b29bf210169..00000000000
--- a/sci-biology/bwa/bwa-0.7.16a.ebuild
+++ /dev/null
@@ -1,36 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit toolchain-funcs
-
-DESCRIPTION="Burrows-Wheeler Alignment Tool, a fast short genomic sequence aligner"
-HOMEPAGE="https://bio-bwa.sourceforge.net/"
-SRC_URI="mirror://sourceforge/bio-bwa/${P}.tar.bz2"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~x64-macos"
-
-RDEPEND="dev-lang/perl"
-
-PATCHES=(
- "${FILESDIR}"/${PN}-0.7.15-Makefile.patch
- "${FILESDIR}"/${PN}-0.7.16a-gcc-10.patch
-)
-DOCS=( NEWS.md README-alt.md README.md )
-
-src_configure() {
- tc-export CC AR
-}
-
-src_install() {
- dobin bwa
-
- exeinto /usr/libexec/${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
deleted file mode 100644
index 39b437a0289..00000000000
--- 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/files/bwa-0.7.16a-gcc-10.patch b/sci-biology/bwa/files/bwa-0.7.16a-gcc-10.patch
deleted file mode 100644
index 40056ffeaaa..00000000000
--- a/sci-biology/bwa/files/bwa-0.7.16a-gcc-10.patch
+++ /dev/null
@@ -1,7 +0,0 @@
---- a/rle.h
-+++ b/rle.h
-@@ -32,3 +32,3 @@ extern "C" {
-
--const uint8_t rle_auxtab[8];
-+extern const uint8_t rle_auxtab[8];
-
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