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authorDavid Seifert <soap@gentoo.org>2020-09-26 12:00:45 +0200
committerDavid Seifert <soap@gentoo.org>2020-09-26 12:00:45 +0200
commit11e7107dfc5e8b95c3af3887c388fa1272b8ddb2 (patch)
tree1b285d6d68c121c2e89eaf70c81746bd031ab74e /sci-biology
parentapp-text/ghostscript-gpl: bump to v9.53.2 (diff)
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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/Manifest1
-rw-r--r--sci-biology/bwa/bwa-0.7.17.ebuild39
-rw-r--r--sci-biology/bwa/files/bwa-0.7.17-Makefile.patch42
-rw-r--r--sci-biology/bwa/files/bwa-0.7.17-gcc-10.patch11
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))