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author | David Seifert <soap@gentoo.org> | 2020-09-26 12:00:45 +0200 |
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committer | David Seifert <soap@gentoo.org> | 2020-09-26 12:00:45 +0200 |
commit | 11e7107dfc5e8b95c3af3887c388fa1272b8ddb2 (patch) | |
tree | 1b285d6d68c121c2e89eaf70c81746bd031ab74e /sci-biology | |
parent | app-text/ghostscript-gpl: bump to v9.53.2 (diff) | |
download | gentoo-11e7107dfc5e8b95c3af3887c388fa1272b8ddb2.tar.gz gentoo-11e7107dfc5e8b95c3af3887c388fa1272b8ddb2.tar.bz2 gentoo-11e7107dfc5e8b95c3af3887c388fa1272b8ddb2.zip |
sci-biology/bwa: Bump version to 0.7.17
Package-Manager: Portage-3.0.8, Repoman-3.0.1
Signed-off-by: David Seifert <soap@gentoo.org>
Diffstat (limited to 'sci-biology')
-rw-r--r-- | sci-biology/bwa/Manifest | 1 | ||||
-rw-r--r-- | sci-biology/bwa/bwa-0.7.17.ebuild | 39 | ||||
-rw-r--r-- | sci-biology/bwa/files/bwa-0.7.17-Makefile.patch | 42 | ||||
-rw-r--r-- | sci-biology/bwa/files/bwa-0.7.17-gcc-10.patch | 11 |
4 files changed, 93 insertions, 0 deletions
diff --git a/sci-biology/bwa/Manifest b/sci-biology/bwa/Manifest index 9da3adbeb40a..4b69e7f04038 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 000000000000..3da06fd74f92 --- /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 000000000000..944369cb75e2 --- /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 000000000000..1babb8356c4a --- /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)) |