From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by finch.gentoo.org (Postfix) with ESMTPS id BDA7D13835A for ; Sat, 26 Sep 2020 10:01:05 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id C9068E0101; Sat, 26 Sep 2020 10:01:04 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [IPv6:2001:470:ea4a:1:5054:ff:fec7:86e4]) (using TLSv1.2 with cipher ECDHE-RSA-AES128-GCM-SHA256 (128/128 bits)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id A1749E0101 for ; Sat, 26 Sep 2020 10:01:04 +0000 (UTC) Received: from oystercatcher.gentoo.org (oystercatcher.gentoo.org [148.251.78.52]) (using TLSv1.2 with cipher ECDHE-RSA-AES128-GCM-SHA256 (128/128 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id 5618D335CEA for ; Sat, 26 Sep 2020 10:01:03 +0000 (UTC) Received: from localhost.localdomain (localhost [IPv6:::1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id B1EDAEC for ; Sat, 26 Sep 2020 10:01:01 +0000 (UTC) From: "David Seifert" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "David Seifert" Message-ID: <1601114445.11e7107dfc5e8b95c3af3887c388fa1272b8ddb2.soap@gentoo> Subject: [gentoo-commits] repo/gentoo:master commit in: sci-biology/bwa/, sci-biology/bwa/files/ X-VCS-Repository: repo/gentoo X-VCS-Files: sci-biology/bwa/Manifest sci-biology/bwa/bwa-0.7.17.ebuild sci-biology/bwa/files/bwa-0.7.17-Makefile.patch sci-biology/bwa/files/bwa-0.7.17-gcc-10.patch X-VCS-Directories: sci-biology/bwa/ sci-biology/bwa/files/ X-VCS-Committer: soap X-VCS-Committer-Name: David Seifert X-VCS-Revision: 11e7107dfc5e8b95c3af3887c388fa1272b8ddb2 X-VCS-Branch: master Date: Sat, 26 Sep 2020 10:01:01 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org X-Auto-Response-Suppress: DR, RN, NRN, OOF, AutoReply X-Archives-Salt: cb4fcbba-dac4-4720-b6c7-ecc1b1ec0dc0 X-Archives-Hash: 25ae6065cce326e7b95c530c55d97ecb commit: 11e7107dfc5e8b95c3af3887c388fa1272b8ddb2 Author: David Seifert gentoo org> AuthorDate: Sat Sep 26 10:00:45 2020 +0000 Commit: David Seifert gentoo org> CommitDate: Sat Sep 26 10:00:45 2020 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=11e7107d sci-biology/bwa: Bump version to 0.7.17 Package-Manager: Portage-3.0.8, Repoman-3.0.1 Signed-off-by: David Seifert gentoo.org> sci-biology/bwa/Manifest | 1 + sci-biology/bwa/bwa-0.7.17.ebuild | 39 +++++++++++++++++++++++ sci-biology/bwa/files/bwa-0.7.17-Makefile.patch | 42 +++++++++++++++++++++++++ sci-biology/bwa/files/bwa-0.7.17-gcc-10.patch | 11 +++++++ 4 files changed, 93 insertions(+) diff --git a/sci-biology/bwa/Manifest b/sci-biology/bwa/Manifest index 9da3adbeb40..4b69e7f0403 100644 --- a/sci-biology/bwa/Manifest +++ b/sci-biology/bwa/Manifest @@ -1 +1,2 @@ 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-0.7.17.ebuild b/sci-biology/bwa/bwa-0.7.17.ebuild new file mode 100644 index 00000000000..3da06fd74f9 --- /dev/null +++ b/sci-biology/bwa/bwa-0.7.17.ebuild @@ -0,0 +1,39 @@ +# 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://github.com/lh3/bwa/" +SRC_URI="https://github.com/lh3/bwa/archive/v${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~x64-macos" + +DEPEND="sys-libs/zlib" +RDEPEND=" + ${DEPEND} + dev-lang/perl" + +PATCHES=( + "${FILESDIR}"/${PN}-0.7.17-Makefile.patch + "${FILESDIR}"/${PN}-0.7.17-gcc-10.patch +) +DOCS=( NEWS.md README-alt.md README.md ) + +src_configure() { + tc-export CC AR +} + +src_install() { + dobin bwa + + exeinto /usr/libexec/${PN} + doexe qualfa2fq.pl xa2multi.pl + + einstalldocs + doman bwa.1 +} diff --git a/sci-biology/bwa/files/bwa-0.7.17-Makefile.patch b/sci-biology/bwa/files/bwa-0.7.17-Makefile.patch new file mode 100644 index 00000000000..944369cb75e --- /dev/null +++ b/sci-biology/bwa/files/bwa-0.7.17-Makefile.patch @@ -0,0 +1,42 @@ +--- a/Makefile ++++ b/Makefile +@@ -1,9 +1,7 @@ +-CC= gcc + #CC= clang --analyze +-CFLAGS= -g -Wall -Wno-unused-function -O2 ++CFLAGS+= -Wall -Wno-unused-function + WRAP_MALLOC=-DUSE_MALLOC_WRAPPERS +-AR= ar +-DFLAGS= -DHAVE_PTHREAD $(WRAP_MALLOC) ++CPPFLAGS+= -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 \ + QSufSort.o bwt_gen.o rope.o rle.o is.o bwtindex.o + AOBJS= bwashm.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o \ +@@ -21,16 +19,13 @@ + + .SUFFIXES:.c .o .cc + +-.c.o: +- $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@ +- + all:$(PROG) + + bwa:libbwa.a $(AOBJS) main.o +- $(CC) $(CFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS) ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS) + + bwamem-lite:libbwa.a example.o +- $(CC) $(CFLAGS) $(DFLAGS) example.o -o $@ -L. -lbwa $(LIBS) ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) example.o -o $@ -L. -lbwa $(LIBS) + + libbwa.a:$(LOBJS) + $(AR) -csru $@ $(LOBJS) +@@ -39,7 +34,7 @@ + rm -f gmon.out *.o a.out $(PROG) *~ *.a + + depend: +- ( LC_ALL=C ; export LC_ALL; makedepend -Y -- $(CFLAGS) $(DFLAGS) -- *.c ) ++ ( LC_ALL=C ; export LC_ALL; makedepend -Y -- $(CFLAGS) $(CPPFLAGS) -- *.c ) + + # DO NOT DELETE THIS LINE -- make depend depends on it. + diff --git a/sci-biology/bwa/files/bwa-0.7.17-gcc-10.patch b/sci-biology/bwa/files/bwa-0.7.17-gcc-10.patch new file mode 100644 index 00000000000..1babb8356c4 --- /dev/null +++ b/sci-biology/bwa/files/bwa-0.7.17-gcc-10.patch @@ -0,0 +1,11 @@ +--- a/rle.h ++++ b/rle.h +@@ -30,7 +30,7 @@ + *** 43+3 codec *** + ******************/ + +-const uint8_t rle_auxtab[8]; ++extern const uint8_t rle_auxtab[8]; + + #define RLE_MIN_SPACE 18 + #define rle_nptr(block) ((uint16_t*)(block))