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

10 files changed, 178 insertions, 0 deletions

diff --git a/biology/Makefile b/biology/Makefile
index db904901b26d..7a81adec4fb3 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -7,6 +7,7 @@
     SUBDIR += artemis
     SUBDIR += avida
     SUBDIR += babel
+    SUBDIR += bcftools
     SUBDIR += biococoa
     SUBDIR += biojava
     SUBDIR += blat
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