9 files changed, 177 insertions, 0 deletions

diff --git a/biology/bcftools/Makefile b/biology/bcftools/Makefile
new file mode 100644
index 000000000000..c975da132524
--- /dev/null
+++ 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>
diff --git a/biology/bcftools/distinfo b/biology/bcftools/distinfo
new file mode 100644
index 000000000000..6a97be056ff3
--- /dev/null
+++ 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
diff --git a/biology/bcftools/files/patch-Makefile b/biology/bcftools/files/patch-Makefile
new file mode 100644
index 000000000000..a0bf28174b0f
--- /dev/null
+++ 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
diff --git a/biology/bcftools/files/patch-plugins_fixploidy.mk b/biology/bcftools/files/patch-plugins_fixploidy.mk
new file mode 100644
index 000000000000..909de819997d
--- /dev/null
+++ 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
diff --git a/biology/bcftools/files/patch-plugins_vcf2sex.mk b/biology/bcftools/files/patch-plugins_vcf2sex.mk
new file mode 100644
index 000000000000..15619f0661db
--- /dev/null
+++ 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
diff --git a/biology/bcftools/files/patch-prob1.c b/biology/bcftools/files/patch-prob1.c
new file mode 100644
index 000000000000..334d1bd37e23
--- /dev/null
+++ 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)
diff --git a/biology/bcftools/files/pkg-message.in b/biology/bcftools/files/pkg-message.in
new file mode 100644
index 000000000000..27c8cb9c4c51
--- /dev/null
+++ b/biology/bcftools/files/pkg-message.in
@@ -0,0 +1,2 @@
+
+Add %%PREFIX%%/bin/samtools_misc to your path to use miscellaneous tools.
diff --git a/biology/bcftools/pkg-descr b/biology/bcftools/pkg-descr
new file mode 100644
index 000000000000..1ef4040b27d7
--- /dev/null
+++ 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/
diff --git a/biology/bcftools/pkg-plist b/biology/bcftools/pkg-plist
new file mode 100644
index 000000000000..0098a1c9afb0
--- /dev/null
+++ 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