New port: biology/bcftools

BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. WWW: http://www.htslib.org/ PR: 199747 Submitted by: cartwright@asu.edu
svn path=/head/; revision=388638
2025-02-03 11:12:13 +00:00 · 2015-06-05 21:01:13 +00:00 · 2015-06-05 21:01:13 +00:00 · def75b1a0f · 2021-03-31 03:12:20 +00:00
commit def75b1a0f
parent 4aa2a93a8b
10 changed files with 178 additions and 0 deletions
--- a/biology/Makefile
+++ b/biology/Makefile
@ -7,6 +7,7 @@
    SUBDIR += artemis
    SUBDIR += avida
    SUBDIR += babel
+    SUBDIR += bcftools
    SUBDIR += biococoa
    SUBDIR += biojava
    SUBDIR += blat
--- a/biology/bcftools/Makefile
+++ b/biology/bcftools/Makefile
@ -0,0 +1,48 @@
+# Created by: Reed A. Cartwright <cartwright@asu.edu>
+# $FreeBSD$
+
+PORTNAME=	bcftools
+PORTVERSION=	1.2
+CATEGORIES=	biology
+
+MAINTAINER=	cartwright@asu.edu
+COMMENT=	Tools for manipulating next-generation sequencing data
+
+LICENSE=	MIT
+LICENSE_FILE=	${WRKSRC}/LICENSE
+
+BUILD_DEPENDS=	htslib>=1.2:${PORTSDIR}/biology/htslib
+LIB_DEPENDS=	libhts.so:${PORTSDIR}/biology/htslib
+
+USE_GITHUB=	yes
+GH_ACCOUNT=	samtools
+
+USES=		gmake shebangfix
+SUB_FILES=	pkg-message
+SHEBANG_FILES=	vcfutils.pl
+
+OPTIONS_DEFINE=	GPL
+GPL_DESC=	Enable modules that rely on GPL code
+OPTIONS_DEFAULT=	GPL
+
+GPL_LIB_DEPENDS=	libgsl.so:${PORTSDIR}/math/gsl
+
+.include <bsd.port.options.mk>
+
+CPPFLAGS+=	-I${LOCALBASE}/include
+LDFLAGS+=	-L${LOCALBASE}/lib
+
+MAKE_ENV=	INSTALL_LIB="${INSTALL_LIB}" \
+			INSTALL_DATA="${INSTALL_DATA}" \
+			INSTALL_PROGRAM="${INSTALL_PROGRAM}" \
+			INSTALL_SCRIPT="${INSTALL_SCRIPT}" \
+			INSTALL_DIR="${MKDIR}"
+
+.if ${PORT_OPTIONS:MGPL}
+MAKE_ENV+=	USE_GPL=1
+LICENSE=	GPLv3
+.endif
+
+PLIST_SUB=	PORTVERSION="${PORTVERSION}"
+
+.include <bsd.port.mk>
--- a/biology/bcftools/distinfo
+++ b/biology/bcftools/distinfo
@ -0,0 +1,2 @@
+SHA256 (samtools-bcftools-1.2_GH0.tar.gz) = 90ccd7dccfb0b2848b71f32fff073c420260e857b7feeb89c1fb4bfaba49bfba
+SIZE (samtools-bcftools-1.2_GH0.tar.gz) = 511625
--- a/biology/bcftools/files/patch-Makefile
+++ b/biology/bcftools/files/patch-Makefile
@ -0,0 +1,84 @@
+--- Makefile.orig	2015-02-02 15:40:17 UTC
+++ Makefile
+@@ -29,14 +29,13 @@ TEST_PROG=  test/test-rbuf
+ all: $(PROG) $(TEST_PROG)
+ 
+ # Adjust $(HTSDIR) to point to your top-level htslib directory
+-HTSDIR = ../htslib
+-include $(HTSDIR)/htslib.mk
+-HTSLIB = $(HTSDIR)/libhts.a
+HTSDIR = $(prefix)/include
+HTSLIB = -lhts
+ BGZIP  = $(HTSDIR)/bgzip
+ TABIX  = $(HTSDIR)/tabix
+ 
+-CC       = gcc
+-CFLAGS   = -g -Wall -Wc++-compat -O2
+CC      ?= cc
+CFLAGS  += -Wall
+ DFLAGS   =
+ OBJS     = main.o vcfindex.o tabix.o \
+            vcfstats.o vcfisec.o vcfmerge.o vcfquery.o vcffilter.o filter.o vcfsom.o \
+@@ -52,22 +51,15 @@ INCLUDES = -I. -I$(HTSDIR)
+ ifdef USE_GPL
+     CFLAGS += -DUSE_GPL
+     OBJS   += polysomy.o
+-    LDLIBS  = -lgsl -lcblas
+    LDLIBS += -lgsl -lgslcblas
+ endif
+ 
+-prefix      = /usr/local
+prefix      = ${STAGEDIR}${PREFIX}
+ exec_prefix = $(prefix)
+ bindir      = $(exec_prefix)/bin
+-mandir      = $(prefix)/share/man
+mandir      = $(prefix)/man
+ man1dir     = $(mandir)/man1
+ 
+-MKDIR_P = mkdir -p
+-INSTALL = install -p
+-INSTALL_PROGRAM = $(INSTALL)
+-INSTALL_DATA    = $(INSTALL) -m 644
+-INSTALL_DIR     = $(MKDIR_P) -m 755
+-
+-
+ all:$(PROG) plugins
+ 
+ # See htslib/Makefile
+@@ -102,8 +94,8 @@ PLUGINC = $(foreach dir, plugins, $(wild
+ PLUGINS = $(PLUGINC:.c=.so)
+ PLUGINM = $(PLUGINC:.c=.mk)
+ 
+-%.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)
+	$(INSTALL_PROGRAM) $(PROG) $(DESTDIR)$(bindir)
+	$(INSTALL_SCRIPT) plot-vcfstats vcfutils.pl $(DESTDIR)$(bindir)/samtools_misc
+ 	$(INSTALL_DATA) doc/bcftools.1 $(DESTDIR)$(man1dir)
+ 
+ clean: testclean clean-plugins
--- a/biology/bcftools/files/patch-plugins_fixploidy.mk
+++ b/biology/bcftools/files/patch-plugins_fixploidy.mk
@ -0,0 +1,7 @@
+--- 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
--- a/biology/bcftools/files/patch-plugins_vcf2sex.mk
+++ b/biology/bcftools/files/patch-plugins_vcf2sex.mk
@ -0,0 +1,7 @@
+--- 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
--- a/biology/bcftools/files/patch-prob1.c
+++ b/biology/bcftools/files/patch-prob1.c
@ -0,0 +1,17 @@
+--- prob1.c.orig	2015-04-28 01:28:23 UTC
+++ prob1.c
+@@ -33,6 +33,14 @@ 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
+#endif
+
+ // #include "kstring.h"
+ // #include "kseq.h"
+ // KSTREAM_INIT(gzFile, gzread, 16384)
--- a/biology/bcftools/files/pkg-message.in
+++ b/biology/bcftools/files/pkg-message.in
@ -0,0 +1,2 @@
+
+Add %%PREFIX%%/bin/samtools_misc to your path to use miscellaneous tools.
--- a/biology/bcftools/pkg-descr
+++ b/biology/bcftools/pkg-descr
@ -0,0 +1,6 @@
+BCFtools is a set of utilities that manipulate variant calls in the
+Variant Call Format (VCF) and its binary counterpart BCF. All
+commands work transparently with both VCFs and BCFs, both
+uncompressed and BGZF-compressed.
+
+WWW: http://www.htslib.org/
--- a/biology/bcftools/pkg-plist
+++ b/biology/bcftools/pkg-plist
@ -0,0 +1,4 @@
+bin/bcftools
+bin/samtools_misc/plot-vcfstats
+bin/samtools_misc/vcfutils.pl
+man/man1/bcftools.1.gz
				`@ -0,0 +1,2 @@`

				`Add %%PREFIX%%/bin/samtools_misc to your path to use miscellaneous tools.`