[gentoo-commits] repo/gentoo:master commit in: sci-biology/bwa/

[gentoo-commits] repo/gentoo:master commit in: sci-biology/bwa/

[David Seifert]

commit:     e04e78ab9f20899f699eb5c871dc77727deac3da
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sat Sep  2 08:07:02 2017 +0000
Commit:     David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sat Sep  2 08:07:02 2017 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=e04e78ab

sci-biology/bwa: Bump to 0.7.16a

Package-Manager: Portage-2.3.8, Repoman-2.3.3

 sci-biology/bwa/Manifest           |  1 +
 sci-biology/bwa/bwa-0.7.16a.ebuild | 34 ++++++++++++++++++++++++++++++++++
 2 files changed, 35 insertions(+)

diff --git a/sci-biology/bwa/Manifest b/sci-biology/bwa/Manifest
index 5589b916838..d2daff2272e 100644
--- a/sci-biology/bwa/Manifest
+++ b/sci-biology/bwa/Manifest
@@ -1,2 +1,3 @@
 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-0.7.16a.ebuild b/sci-biology/bwa/bwa-0.7.16a.ebuild
new file mode 100644
index 00000000000..21fe67143bd
--- /dev/null
+++ b/sci-biology/bwa/bwa-0.7.16a.ebuild
@@ -0,0 +1,34 @@
+# 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="https://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
+}

[gentoo-commits] repo/gentoo:master commit in: sci-biology/bwa/

[Sam James]

commit:     372ec6970bfb31622d7a32f5830bd5d1c3a58cfb
Author:     Sam James <sam <AT> gentoo <DOT> org>
AuthorDate: Sat Jul 30 08:27:01 2022 +0000
Commit:     Sam James <sam <AT> gentoo <DOT> org>
CommitDate: Sat Jul 30 08:27:01 2022 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=372ec697

sci-biology/bwa: add github upstream metadata

Signed-off-by: Sam James <sam <AT> gentoo.org>

 sci-biology/bwa/metadata.xml | 15 ++++++++-------
 1 file changed, 8 insertions(+), 7 deletions(-)

diff --git a/sci-biology/bwa/metadata.xml b/sci-biology/bwa/metadata.xml
index d55fb9717ad3..21fbf032d0bf 100644
--- a/sci-biology/bwa/metadata.xml
+++ b/sci-biology/bwa/metadata.xml
@@ -1,11 +1,12 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "https://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>
+	<maintainer type="project">
+		<email>sci-biology@gentoo.org</email>
+		<name>Gentoo Biology Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">lh3/bwa</remote-id>
+		<remote-id type="sourceforge">bio-bwa</remote-id>
+	</upstream>
 </pkgmetadata>

[gentoo-commits] repo/gentoo:master commit in: sci-biology/bwa/

[Sam James]

commit:     8479cf13101c1bcc4bf088768449a617f0146c8a
Author:     Eli Schwartz <eschwartz93 <AT> gmail <DOT> com>
AuthorDate: Thu Feb 29 04:26:03 2024 +0000
Commit:     Sam James <sam <AT> gentoo <DOT> org>
CommitDate: Thu Feb 29 04:47:16 2024 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=8479cf13

sci-biology/bwa: mark as LTO-unsafe

Closes: https://bugs.gentoo.org/862255
Signed-off-by: Eli Schwartz <eschwartz93 <AT> gmail.com>
Signed-off-by: Sam James <sam <AT> gentoo.org>

 sci-biology/bwa/bwa-0.7.17.ebuild | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/sci-biology/bwa/bwa-0.7.17.ebuild b/sci-biology/bwa/bwa-0.7.17.ebuild
index 3da06fd74f92..e1b6dbb6184e 100644
--- a/sci-biology/bwa/bwa-0.7.17.ebuild
+++ b/sci-biology/bwa/bwa-0.7.17.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2024 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
 
-inherit toolchain-funcs
+inherit flag-o-matic toolchain-funcs
 
 DESCRIPTION="Burrows-Wheeler Alignment Tool, a fast short genomic sequence aligner"
 HOMEPAGE="https://github.com/lh3/bwa/"
@@ -25,6 +25,11 @@ PATCHES=(
 DOCS=( NEWS.md README-alt.md README.md )
 
 src_configure() {
+	# -Werror=lto-type-mismatch
+	# https://bugs.gentoo.org/862255
+	# https://github.com/lh3/bwa/issues/411
+	filter-lto
+
 	tc-export CC AR
 }