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commit: 11e7107dfc5e8b95c3af3887c388fa1272b8ddb2 |
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Author: David Seifert <soap <AT> gentoo <DOT> org> |
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AuthorDate: Sat Sep 26 10:00:45 2020 +0000 |
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Commit: David Seifert <soap <AT> gentoo <DOT> org> |
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CommitDate: Sat Sep 26 10:00:45 2020 +0000 |
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URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=11e7107d |
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|
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sci-biology/bwa: Bump version to 0.7.17 |
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|
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Package-Manager: Portage-3.0.8, Repoman-3.0.1 |
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Signed-off-by: David Seifert <soap <AT> gentoo.org> |
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|
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sci-biology/bwa/Manifest | 1 + |
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sci-biology/bwa/bwa-0.7.17.ebuild | 39 +++++++++++++++++++++++ |
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sci-biology/bwa/files/bwa-0.7.17-Makefile.patch | 42 +++++++++++++++++++++++++ |
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sci-biology/bwa/files/bwa-0.7.17-gcc-10.patch | 11 +++++++ |
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4 files changed, 93 insertions(+) |
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|
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diff --git a/sci-biology/bwa/Manifest b/sci-biology/bwa/Manifest |
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index 9da3adbeb40..4b69e7f0403 100644 |
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--- a/sci-biology/bwa/Manifest |
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+++ b/sci-biology/bwa/Manifest |
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@@ -1 +1,2 @@ |
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DIST bwa-0.7.16a.tar.bz2 190773 BLAKE2B e1064381b6b1aa4c9b78d12222c7b783a55676a163b94ad8596a2af64c9b0d60bbebd8e840aaa13b25e1ca4f10466c2c39c99830f1ca58e558d724d1ad583944 SHA512 8bbe223f79efd328d66adb88baf995e894f5944aad912ac1b464dc84dc9b4e22ddf77b60dcbe468e0eedc344ee58d08dc498777f0d2794a2c1e0ddd33dad606d |
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+DIST bwa-0.7.17.tar.gz 232593 BLAKE2B fa48aad72a47547d66c767e2e2a5aadfcfc7c77c517410812230f51a2222ee66bb04383b068036b696af0a57b04b35e97bed11e3c44793aa899a8c0807f3df5e SHA512 114e61b7cc5edcb67172d1eca7be1fa670ea33dd48b5c02c98318e254871363775c0dab327fd7ee7023200a5fedc745fa01cbe0fd9550d783f091d4df6926f48 |
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|
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diff --git a/sci-biology/bwa/bwa-0.7.17.ebuild b/sci-biology/bwa/bwa-0.7.17.ebuild |
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new file mode 100644 |
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index 00000000000..3da06fd74f9 |
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--- /dev/null |
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+++ b/sci-biology/bwa/bwa-0.7.17.ebuild |
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@@ -0,0 +1,39 @@ |
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+# Copyright 1999-2020 Gentoo Authors |
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+# Distributed under the terms of the GNU General Public License v2 |
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+ |
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+EAPI=7 |
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+ |
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+inherit toolchain-funcs |
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+ |
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+DESCRIPTION="Burrows-Wheeler Alignment Tool, a fast short genomic sequence aligner" |
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+HOMEPAGE="https://github.com/lh3/bwa/" |
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+SRC_URI="https://github.com/lh3/bwa/archive/v${PV}.tar.gz -> ${P}.tar.gz" |
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+ |
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+LICENSE="GPL-3" |
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+SLOT="0" |
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+KEYWORDS="~amd64 ~x86 ~x64-macos" |
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+ |
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+DEPEND="sys-libs/zlib" |
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+RDEPEND=" |
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+ ${DEPEND} |
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+ dev-lang/perl" |
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+ |
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+PATCHES=( |
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+ "${FILESDIR}"/${PN}-0.7.17-Makefile.patch |
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+ "${FILESDIR}"/${PN}-0.7.17-gcc-10.patch |
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+) |
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+DOCS=( NEWS.md README-alt.md README.md ) |
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+ |
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+src_configure() { |
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+ tc-export CC AR |
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+} |
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+ |
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+src_install() { |
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+ dobin bwa |
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+ |
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+ exeinto /usr/libexec/${PN} |
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+ doexe qualfa2fq.pl xa2multi.pl |
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+ |
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+ einstalldocs |
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+ doman bwa.1 |
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+} |
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|
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diff --git a/sci-biology/bwa/files/bwa-0.7.17-Makefile.patch b/sci-biology/bwa/files/bwa-0.7.17-Makefile.patch |
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new file mode 100644 |
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index 00000000000..944369cb75e |
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--- /dev/null |
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+++ b/sci-biology/bwa/files/bwa-0.7.17-Makefile.patch |
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@@ -0,0 +1,42 @@ |
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+--- a/Makefile |
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++++ b/Makefile |
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+@@ -1,9 +1,7 @@ |
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+-CC= gcc |
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+ #CC= clang --analyze |
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+-CFLAGS= -g -Wall -Wno-unused-function -O2 |
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++CFLAGS+= -Wall -Wno-unused-function |
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+ WRAP_MALLOC=-DUSE_MALLOC_WRAPPERS |
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+-AR= ar |
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+-DFLAGS= -DHAVE_PTHREAD $(WRAP_MALLOC) |
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++CPPFLAGS+= -DHAVE_PTHREAD $(WRAP_MALLOC) |
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+ 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 \ |
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+ QSufSort.o bwt_gen.o rope.o rle.o is.o bwtindex.o |
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+ AOBJS= bwashm.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o \ |
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+@@ -21,16 +19,13 @@ |
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+ |
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+ .SUFFIXES:.c .o .cc |
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+ |
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+-.c.o: |
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+- $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@ |
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+- |
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+ all:$(PROG) |
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+ |
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+ bwa:libbwa.a $(AOBJS) main.o |
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+- $(CC) $(CFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS) |
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++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS) |
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+ |
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+ bwamem-lite:libbwa.a example.o |
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+- $(CC) $(CFLAGS) $(DFLAGS) example.o -o $@ -L. -lbwa $(LIBS) |
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++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) example.o -o $@ -L. -lbwa $(LIBS) |
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+ |
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+ libbwa.a:$(LOBJS) |
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+ $(AR) -csru $@ $(LOBJS) |
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+@@ -39,7 +34,7 @@ |
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+ rm -f gmon.out *.o a.out $(PROG) *~ *.a |
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+ |
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+ depend: |
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+- ( LC_ALL=C ; export LC_ALL; makedepend -Y -- $(CFLAGS) $(DFLAGS) -- *.c ) |
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++ ( LC_ALL=C ; export LC_ALL; makedepend -Y -- $(CFLAGS) $(CPPFLAGS) -- *.c ) |
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+ |
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+ # DO NOT DELETE THIS LINE -- make depend depends on it. |
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+ |
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|
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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 |
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new file mode 100644 |
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index 00000000000..1babb8356c4 |
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--- /dev/null |
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+++ b/sci-biology/bwa/files/bwa-0.7.17-gcc-10.patch |
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@@ -0,0 +1,11 @@ |
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+--- a/rle.h |
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++++ b/rle.h |
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+@@ -30,7 +30,7 @@ |
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+ *** 43+3 codec *** |
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+ ******************/ |
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+ |
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+-const uint8_t rle_auxtab[8]; |
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++extern const uint8_t rle_auxtab[8]; |
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+ |
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+ #define RLE_MIN_SPACE 18 |
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+ #define rle_nptr(block) ((uint16_t*)(block)) |