Attachment 164519 Details for Bug 205526 – Patch to upgrade biology/bcftools to 1.3

Patch to upgrade biology/bcftools to 1.3

bcftools-1.3.diff (text/plain), 11.69 KB, created by cartwright on 2015-12-22 23:26:43 UTC

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Creator: cartwright

Created: 2015-12-22 23:26:43 UTC

Size: 11.69 KB

patch

obsolete

>Index: Makefile
>===================================================================
>--- Makefile	(revision 403942)
>+++ Makefile	(working copy)
>@@ -2,7 +2,7 @@
> # $FreeBSD$
> 
> PORTNAME=	bcftools
>-PORTVERSION=	1.2
>+PORTVERSION=	1.3
> CATEGORIES=	biology
> 
> MAINTAINER=	cartwright@asu.edu
>@@ -11,15 +11,17 @@
> LICENSE=	MIT
> LICENSE_FILE=	${WRKSRC}/LICENSE
> 
>-BUILD_DEPENDS=	htslib>=1.2:${PORTSDIR}/biology/htslib
>+BUILD_DEPENDS=	htslib>=1.3:${PORTSDIR}/biology/htslib
> LIB_DEPENDS=	libhts.so:${PORTSDIR}/biology/htslib
>+TEST_DEPENDS=	bash:${PORTSDIR}/shells/bash
> 
> USE_GITHUB=	yes
> GH_ACCOUNT=	samtools
> 
>-USES=		gmake shebangfix
>+USES=		gmake perl5 shebangfix
>+USE_PERL5=	test
> SUB_FILES=	pkg-message
>-SHEBANG_FILES=	vcfutils.pl
>+SHEBANG_FILES=	vcfutils.pl plot-vcfstats plugins/color-chrs.pl test/test.pl
> 
> OPTIONS_DEFINE=	GPL
> GPL_DESC=	Enable modules that rely on GPL code
>@@ -33,10 +35,10 @@
> LDFLAGS+=	-L${LOCALBASE}/lib
> 
> MAKE_ENV=	INSTALL_LIB="${INSTALL_LIB}" \
>-			INSTALL_DATA="${INSTALL_DATA}" \
>-			INSTALL_PROGRAM="${INSTALL_PROGRAM}" \
>-			INSTALL_SCRIPT="${INSTALL_SCRIPT}" \
>-			INSTALL_DIR="${MKDIR}"
>+		INSTALL_DATA="${INSTALL_DATA}" \
>+		INSTALL_PROGRAM="${INSTALL_PROGRAM}" \
>+		INSTALL_SCRIPT="${INSTALL_SCRIPT}" \
>+		INSTALL_DIR="${MKDIR}"
> 
> .if ${PORT_OPTIONS:MGPL}
> MAKE_ENV+=	USE_GPL=1
>@@ -45,4 +47,6 @@
> 
> PLIST_SUB=	PORTVERSION="${PORTVERSION}"
> 
>+TEST_TARGET=	test
>+
> .include <bsd.port.mk>
>Index: distinfo
>===================================================================
>--- distinfo	(revision 403942)
>+++ distinfo	(working copy)
>@@ -1,2 +1,2 @@
>-SHA256 (samtools-bcftools-1.2_GH0.tar.gz) = 90ccd7dccfb0b2848b71f32fff073c420260e857b7feeb89c1fb4bfaba49bfba
>-SIZE (samtools-bcftools-1.2_GH0.tar.gz) = 511625
>+SHA256 (samtools-bcftools-1.3_GH0.tar.gz) = 3f4d4bf68637070cb7dbb5d5619ece7e3315727e651eab751d849085439b11d8
>+SIZE (samtools-bcftools-1.3_GH0.tar.gz) = 943041
>Index: files/patch-Makefile
>===================================================================
>--- files/patch-Makefile	(revision 403942)
>+++ files/patch-Makefile	(working copy)
>@@ -1,6 +1,6 @@
>---- Makefile.orig	2015-02-02 15:40:17 UTC
>+--- Makefile.orig	2015-12-15 21:42:34 UTC
> +++ Makefile
>-@@ -29,14 +29,13 @@ TEST_PROG=  test/test-rbuf
>+@@ -29,16 +29,15 @@ TEST_PROG=  test/test-rbuf
>  all: $(PROG) $(TEST_PROG)
>  
>  # Adjust $(HTSDIR) to point to your top-level htslib directory
>@@ -7,24 +7,30 @@
> -HTSDIR = ../htslib
> -include $(HTSDIR)/htslib.mk
> -HTSLIB = $(HTSDIR)/libhts.a
>+-BGZIP  = $(HTSDIR)/bgzip
>+-TABIX  = $(HTSDIR)/tabix
> +HTSDIR = $(prefix)/include
> +HTSLIB = -lhts
>- BGZIP  = $(HTSDIR)/bgzip
>- TABIX  = $(HTSDIR)/tabix
>++BGZIP  = $(HTSDIR)/../bin/bgzip
>++TABIX  = $(HTSDIR)/../bin/tabix
>  
> -CC       = gcc
>+-CPPFLAGS =
> -CFLAGS   = -g -Wall -Wc++-compat -O2
>-+CC      ?= cc
>-+CFLAGS  += -Wall
>- DFLAGS   =
>+-LDFLAGS  =
>++CC       ?= cc
>++CPPFLAGS +=
>++CFLAGS   += -Wall
>++LDFLAGS  +=
>+ LIBS     =
>+ 
>  OBJS     = main.o vcfindex.o tabix.o \
>-            vcfstats.o vcfisec.o vcfmerge.o vcfquery.o vcffilter.o filter.o vcfsom.o \
>-@@ -52,22 +51,15 @@ INCLUDES = -I. -I$(HTSDIR)
>+@@ -57,26 +56,20 @@ GSL_LIBS       =
>  ifdef USE_GPL
>-     CFLAGS += -DUSE_GPL
>-     OBJS   += polysomy.o
>--    LDLIBS  = -lgsl -lcblas
>-+    LDLIBS += -lgsl -lgslcblas
>+     EXTRA_CPPFLAGS += -DUSE_GPL
>+     OBJS += polysomy.o peakfit.o
>+-    GSL_LIBS = -lgsl -lcblas
>++    GSL_LIBS = -lgsl -lgslcblas
>  endif
>  
> -prefix      = /usr/local
>@@ -31,10 +37,15 @@
> +prefix      = ${STAGEDIR}${PREFIX}
>  exec_prefix = $(prefix)
>  bindir      = $(exec_prefix)/bin
>+ libdir      = $(exec_prefix)/lib
>+ libexecdir  = $(exec_prefix)/libexec
> -mandir      = $(prefix)/share/man
> +mandir      = $(prefix)/man
>  man1dir     = $(mandir)/man1
>  
>+ plugindir   = $(libexecdir)/bcftools
>+ pluginpath  = $(plugindir)
>+ 
> -MKDIR_P = mkdir -p
> -INSTALL = install -p
> -INSTALL_PROGRAM = $(INSTALL)
>@@ -41,44 +52,27 @@
> -INSTALL_DATA    = $(INSTALL) -m 644
> -INSTALL_DIR     = $(MKDIR_P) -m 755
> -
>--
>+ MISC_PROGRAMS = plot-vcfstats vcfutils.pl plugins/color-chrs.pl
>+ 
>  all:$(PROG) plugins
>+@@ -181,7 +174,7 @@ test/test-rbuf: test/test-rbuf.o
>+ 	$(CC) $(LDFLAGS) -o $@ $^ -lm $(LIBS)
>  
>- # See htslib/Makefile
>-@@ -102,8 +94,8 @@ PLUGINC = $(foreach dir, plugins, $(wild
>- PLUGINS = $(PLUGINC:.c=.so)
>- PLUGINM = $(PLUGINC:.c=.mk)
>+ bcftools: $(HTSLIB) $(OBJS)
>+-	$(CC) -rdynamic $(LDFLAGS) -o $@ $(OBJS) $(HTSLIB) -lpthread -lz -lm -ldl $(GSL_LIBS) $(LIBS)
>++	$(CC) -rdynamic $(LDFLAGS) -o $@ $(OBJS) $(HTSLIB) -pthread -lz -lm $(GSL_LIBS) $(LIBS)
>  
>--%.so: %.c version.h version.c $(HTSDIR)/libhts.so
>--	$(CC) $(CFLAGS) $(INCLUDES) -fPIC -shared -o $@ version.c $< -L$(HTSDIR) -lhts
>-+%.so: %.c version.h version.c
>-+	$(CC) $(CFLAGS) $(LDFLAGS) $(INCLUDES) -fPIC -shared -o $@ version.c $<  -lhts
>- 
>- -include $(PLUGINM)
>- 
>-@@ -156,10 +148,10 @@ version.o: version.h version.c
>- test/test-rbuf.o: test/test-rbuf.c rbuf.h
>- 
>- test/test-rbuf: test/test-rbuf.o
>--	$(CC) $(CFLAGS) -o $@ -lm -ldl $<
>-+	$(CC) $(CFLAGS) -o $@ -lm $<
>- 
>--bcftools: $(HTSLIB) $(OBJS)
>--	$(CC) $(CFLAGS) -o $@ $(OBJS) $(HTSLIB) -lpthread -lz -lm -ldl $(LDLIBS)
>-+bcftools: $(OBJS)
>-+	$(CC) -pthread $(CFLAGS) $(LDFLAGS) -o $@ $(OBJS) $(HTSLIB)  -lz -lm $(LDLIBS)
>- 
>  doc/bcftools.1: doc/bcftools.txt
>  	cd doc && a2x -adate="$(DOC_DATE)" -aversion=$(DOC_VERSION) --doctype manpage --format manpage bcftools.txt
>-@@ -170,8 +162,9 @@ doc/bcftools.html: doc/bcftools.txt
>- docs: doc/bcftools.1 doc/bcftools.html
>- 
>- install: $(PROG) doc/bcftools.1
>--	$(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(man1dir)
>--	$(INSTALL_PROGRAM) $(PROG) plot-vcfstats vcfutils.pl $(DESTDIR)$(bindir)
>-+	$(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(bindir)/samtools_misc $(DESTDIR)$(man1dir)
>+@@ -198,8 +191,9 @@ docs: doc/bcftools.1 doc/bcftools.html
>+ # Since there is no make dependency, bcftools.1 can be out-of-date and
>+ # make docs can be run to update if asciidoc is available
>+ install: $(PROG)
>+-	$(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(man1dir) $(DESTDIR)$(plugindir)
>+-	$(INSTALL_PROGRAM) $(PROG) $(MISC_PROGRAMS) $(DESTDIR)$(bindir)
>++	$(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(bindir)/samtools_misc $(DESTDIR)$(man1dir) $(DESTDIR)$(plugindir)
> +	$(INSTALL_PROGRAM) $(PROG) $(DESTDIR)$(bindir)
>-+	$(INSTALL_SCRIPT) plot-vcfstats vcfutils.pl $(DESTDIR)$(bindir)/samtools_misc
>++	$(INSTALL_SCRIPT) $(MISC_PROGRAMS) $(DESTDIR)$(bindir)/samtools_misc
>  	$(INSTALL_DATA) doc/bcftools.1 $(DESTDIR)$(man1dir)
>+ 	$(INSTALL_PROGRAM) plugins/*.so $(DESTDIR)$(plugindir)
>  
>- clean: testclean clean-plugins
>Index: files/patch-plugins_fixploidy.mk
>===================================================================
>--- files/patch-plugins_fixploidy.mk	(revision 403942)
>+++ files/patch-plugins_fixploidy.mk	(working copy)
>@@ -1,7 +0,0 @@
>---- plugins/fixploidy.mk.orig	2015-02-02 15:40:17 UTC
>-+++ plugins/fixploidy.mk
>-@@ -1,2 +1,2 @@
>--plugins/fixploidy.so: plugins/fixploidy.c version.h version.c ploidy.h ploidy.c $(HTSDIR)/libhts.so
>--	$(CC) $(CFLAGS) $(INCLUDES) -fPIC -shared -o $@ ploidy.c version.c $< -L$(HTSDIR) -lhts
>-+plugins/fixploidy.so: plugins/fixploidy.c version.h version.c ploidy.h ploidy.c
>-+	$(CC) $(CFLAGS) $(LDFLAGS) $(INCLUDES) -fPIC -shared -o $@ ploidy.c version.c $< -lhts
>Index: files/patch-plugins_vcf2sex.mk
>===================================================================
>--- files/patch-plugins_vcf2sex.mk	(revision 403942)
>+++ files/patch-plugins_vcf2sex.mk	(working copy)
>@@ -1,7 +0,0 @@
>---- plugins/vcf2sex.mk.orig	2015-02-02 15:40:17 UTC
>-+++ plugins/vcf2sex.mk
>-@@ -1,2 +1,2 @@
>--plugins/vcf2sex.so: plugins/vcf2sex.c version.h version.c ploidy.h ploidy.c $(HTSDIR)/libhts.so
>--	$(CC) $(CFLAGS) $(INCLUDES) -fPIC -shared -o $@ ploidy.c version.c $< -L$(HTSDIR) -lhts
>-+plugins/vcf2sex.so: plugins/vcf2sex.c version.h version.c ploidy.h ploidy.c
>-+	$(CC) $(CFLAGS) $(LDFLAGS) $(INCLUDES) -fPIC -shared -o $@ ploidy.c version.c $< -lhts
>Index: files/patch-prob1.c
>===================================================================
>--- files/patch-prob1.c	(revision 403942)
>+++ files/patch-prob1.c	(working copy)
>@@ -1,15 +1,13 @@
>---- prob1.c.orig	2015-04-28 01:28:23 UTC
>+--- prob1.c.orig	2015-12-15 21:42:34 UTC
> +++ prob1.c
>-@@ -33,6 +33,14 @@ THE SOFTWARE.  */
>+@@ -33,6 +33,12 @@ THE SOFTWARE.  */
>  #include <zlib.h>
>  #include "prob1.h"
>  
> +#include <sys/param.h>
>-+#ifdef __FreeBSD__
>-+#	if __FreeBSD_version < 1000034
>-+#		define logl(x) log(x)
>-+#		define expl(x) exp(x)
>-+#	endif
>++#if defined(__FreeBSD__) && (__FreeBSD_version < 1000034)
>++#	define logl(x) log(x)
>++#	define expl(x) exp(x)
> +#endif
> +
>  // #include "kstring.h"
>Index: files/patch-test_test.pl
>===================================================================
>--- files/patch-test_test.pl	(revision 0)
>+++ files/patch-test_test.pl	(working copy)
>@@ -0,0 +1,29 @@
>+--- test/test.pl.orig	2015-12-22 22:45:13 UTC
>++++ test/test.pl
>+@@ -290,7 +290,7 @@ sub _cmd
>+     else
>+     {
>+         # child
>+-        exec('/bin/bash', '-o','pipefail','-c', $cmd) or error("Cannot execute the command [/bin/sh -o pipefail -c $cmd]: $!");
>++        exec('/usr/local/bin/bash', '-o','pipefail','-c', $cmd) or error("Cannot execute the command [/usr/local/bin/sh -o pipefail -c $cmd]: $!");
>+     }
>+     return ($? >> 8, join('',@out));
>+ }
>+@@ -657,7 +657,7 @@ sub test_usage
>+     my $command = $args{cmd};
>+     my $commandpath = $$opts{bin}."/".$command;
>+     my ($ret,$out) = _cmd("$commandpath $args{redirection} 2>&1");
>+-    if ( $out =~ m/\/bin\/bash.*no.*such/i ) { failed($opts,$test,"could not run $commandpath: $out"); return; }
>++    if ( $out =~ m/\/usr\/local\/bin\/bash.*no.*such/i ) { failed($opts,$test,"could not run $commandpath: $out"); return; }
>+ 
>+     my @sections = ($out =~ m/(^[A-Za-z]+.*?)(?:(?=^[A-Za-z]+:)|\z)/msg);
>+ 
>+@@ -708,7 +708,7 @@ sub test_usage_subcommand
>+     my $subcommand = $args{subcmd};
>+     my $commandpath = $$opts{bin}."/".$command;
>+     my ($ret,$out) = _cmd("$commandpath $subcommand $args{redirection} 2>&1");
>+-    if ( $out =~ m/\/bin\/bash.*no.*such/i ) { failed($opts,$test,"could not run $commandpath $subcommand: $out"); return; }
>++    if ( $out =~ m/\/usr\/local\/bin\/bash.*no.*such/i ) { failed($opts,$test,"could not run $commandpath $subcommand: $out"); return; }
>+ 
>+     my @sections = ($out =~ m/(^[A-Za-z]+.*?)(?:(?=^[A-Za-z]+:)|\z)/msg);
>+ 
>
>Property changes on: files/patch-test_test.pl
>___________________________________________________________________
>Added: fbsd:nokeywords
>## -0,0 +1 ##
>+yes
>\ No newline at end of property
>Added: svn:eol-style
>## -0,0 +1 ##
>+native
>\ No newline at end of property
>Added: svn:mime-type
>## -0,0 +1 ##
>+text/plain
>\ No newline at end of property
>Index: files/pkg-message.in
>===================================================================
>--- files/pkg-message.in	(revision 403942)
>+++ files/pkg-message.in	(working copy)
>@@ -1,2 +1,3 @@
>+The miscellaneous tools included with Bcftools have been installed to %%PREFIX%%/bin/samtools_misc. Add that directory to your path if you want to use these tools.
> 
>-Add %%PREFIX%%/bin/samtools_misc to your path to use miscellaneous tools.
>+Some of these tools depend on Perl5, and it will need to be installed to use them.
>\ No newline at end of file
>Index: pkg-plist
>===================================================================
>--- pkg-plist	(revision 403942)
>+++ pkg-plist	(working copy)
>@@ -1,4 +1,18 @@
> bin/bcftools
>+bin/samtools_misc/color-chrs.pl
> bin/samtools_misc/plot-vcfstats
> bin/samtools_misc/vcfutils.pl
>+libexec/bcftools/color-chrs.so
>+libexec/bcftools/counts.so
>+libexec/bcftools/dosage.so
>+libexec/bcftools/fill-AN-AC.so
>+libexec/bcftools/fill-tags.so
>+libexec/bcftools/fixploidy.so
>+libexec/bcftools/frameshifts.so
>+libexec/bcftools/impute-info.so
>+libexec/bcftools/mendelian.so
>+libexec/bcftools/missing2ref.so
>+libexec/bcftools/setGT.so
>+libexec/bcftools/tag2tag.so
>+libexec/bcftools/vcf2sex.so
> man/man1/bcftools.1.gz

Flags:

vlad-fbsd: maintainer-approval+

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Attachments on bug 205526: 164519 | 164520 | 164521