7 files changed, 168 insertions, 0 deletions

diff --git a/biology/samtools/Makefile b/biology/samtools/Makefile
new file mode 100644
index 000000000000..50376b733fae
--- /dev/null
+++ b/biology/samtools/Makefile
@@ -0,0 +1,34 @@
+# Created by: Reed A. Cartwright <cartwright@asu.edu>
+# $FreeBSD$
+
+PORTNAME=	samtools
+PORTVERSION=	1.1
+CATEGORIES=	biology
+
+MAINTAINER=	cartwright@asu.edu
+COMMENT=	Tools for manipulating next-generation sequencing data
+
+LICENSE=	MIT
+LICENSE_FILE=	${WRKSRC}/LICENSE
+
+LIB_DEPENDS=	libhts.so:${PORTSDIR}/biology/htslib
+
+USE_GITHUB=	yes
+GH_ACCOUNT=	samtools
+GH_COMMIT=	34c6691
+
+USES=		gmake
+SUB_FILES=	pkg-message
+
+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="${MKDIR}"
+
+PLIST_SUB=	PORTVERSION="${PORTVERSION}"
+
+.include <bsd.port.mk>
diff --git a/biology/samtools/distinfo b/biology/samtools/distinfo
new file mode 100644
index 000000000000..c77ae42c8be3
--- /dev/null
+++ b/biology/samtools/distinfo
@@ -0,0 +1,2 @@
+SHA256 (samtools-1.1.tar.gz) = adf674bef85e6ffd88d19178a46f229fc033c7302610d5a51ef9709dd0346c59
+SIZE (samtools-1.1.tar.gz) = 4321336
diff --git a/biology/samtools/files/patch-Makefile b/biology/samtools/files/patch-Makefile
new file mode 100644
index 000000000000..372c29263ce2
--- /dev/null
+++ b/biology/samtools/files/patch-Makefile
@@ -0,0 +1,85 @@
+--- Makefile.orig	2014-09-19 15:51:42 UTC
++++ Makefile
+@@ -21,12 +21,12 @@
+ # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+ # DEALINGS IN THE SOFTWARE.
+ 
+-CC       = gcc
+-CPPFLAGS = $(DFLAGS) $(INCLUDES)
+-CFLAGS   = -g -Wall -O2
+-LDFLAGS  =
+-LDLIBS   =
+-DFLAGS=     -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1
++CC       ?= cc
++CPPFLAGS += $(DFLAGS) $(INCLUDES)
++CFLAGS   += -Wall -Wno-unused-function -Wno-implicit-function-declaration
++LDFLAGS  +=
++LDLIBS   +=
++DFLAGS=     -D_CURSES_LIB=1
+ LOBJS=      bam_aux.o bam.o bam_import.o sam.o \
+             sam_header.o bam_plbuf.o
+ AOBJS=      bam_index.o bam_plcmd.o sam_view.o \
+@@ -39,19 +39,12 @@ AOBJS=      bam_index.o bam_plcmd.o sam_
+ INCLUDES=   -I. -I$(HTSDIR)
+ LIBCURSES=  -lcurses # -lXCurses
+ 
+-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
+-
+-
+ PROGRAMS = samtools
+ 
+ BUILT_MISC_PROGRAMS = \
+@@ -59,7 +52,6 @@ BUILT_MISC_PROGRAMS = \
+ 	misc/md5fa misc/md5sum-lite misc/wgsim
+ 
+ MISC_PROGRAMS = \
+-	$(BUILT_MISC_PROGRAMS) \
+ 	misc/blast2sam.pl misc/bowtie2sam.pl misc/export2sam.pl \
+ 	misc/interpolate_sam.pl misc/novo2sam.pl \
+ 	misc/plot-bamstats misc/psl2sam.pl \
+@@ -82,9 +74,8 @@ all: $(PROGRAMS) $(BUILT_MISC_PROGRAMS) 
+ 
+ 
+ # 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  = $(HTSDIR)/bgzip
+ 
+ 
+@@ -121,7 +112,7 @@ lib:libbam.a
+ libbam.a:$(LOBJS)
+ 	$(AR) -csru $@ $(LOBJS)
+ 
+-samtools: $(AOBJS) libbam.a $(HTSLIB)
++samtools: $(AOBJS) libbam.a
+ 	$(CC) -pthread $(LDFLAGS) -o $@ $(AOBJS) libbam.a $(HTSLIB) $(LDLIBS) $(LIBCURSES) -lm -lz
+ 
+ bam_h = bam.h $(htslib_bgzf_h) $(htslib_sam_h)
+@@ -269,8 +260,10 @@ misc/md5sum-lite.o: misc/md5.c misc/md5.
+ 
+ 
+ install: $(PROGRAMS) $(BUILT_MISC_PROGRAMS)
+-	$(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(man1dir)
+-	$(INSTALL_PROGRAM) $(PROGRAMS) $(MISC_PROGRAMS) $(DESTDIR)$(bindir)
++	$(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(bindir)/samtools_misc $(DESTDIR)$(man1dir) 
++	$(INSTALL_PROGRAM) $(PROGRAMS) $(DESTDIR)$(bindir)
++	$(INSTALL_PROGRAM) $(BUILT_MISC_PROGRAMS) $(DESTDIR)$(bindir)/samtools_misc
++	$(INSTALL_SCRIPT) $(MISC_PROGRAMS) $(DESTDIR)$(bindir)/samtools_misc
+ 	$(INSTALL_DATA) samtools.1 $(DESTDIR)$(man1dir)
+ 
+ 
diff --git a/biology/samtools/files/patch-errmod.c b/biology/samtools/files/patch-errmod.c
new file mode 100644
index 000000000000..c241fd38a674
--- /dev/null
+++ b/biology/samtools/files/patch-errmod.c
@@ -0,0 +1,18 @@
+--- errmod.c.orig	2014-12-15 20:22:22 UTC
++++ errmod.c
+@@ -24,6 +24,15 @@ FROM, OUT OF OR IN CONNECTION WITH THE S
+ DEALINGS IN THE SOFTWARE.  */
+ 
+ #include <math.h>
++
++#include <sys/param.h>
++#ifdef __FreeBSD__
++#	if __FreeBSD_version < 1000034
++#		define logl(x) log(x)
++#		define expl(x) exp(x)
++#	endif
++#endif
++
+ #include "errmod.h"
+ #include "htslib/ksort.h"
+ KSORT_INIT_GENERIC(uint16_t)
diff --git a/biology/samtools/files/pkg-message.in b/biology/samtools/files/pkg-message.in
new file mode 100644
index 000000000000..27c8cb9c4c51
--- /dev/null
+++ b/biology/samtools/files/pkg-message.in
@@ -0,0 +1,2 @@
+
+Add %%PREFIX%%/bin/samtools_misc to your path to use miscellaneous tools.
diff --git a/biology/samtools/pkg-descr b/biology/samtools/pkg-descr
new file mode 100644
index 000000000000..ee9b6e47fa84
--- /dev/null
+++ b/biology/samtools/pkg-descr
@@ -0,0 +1,5 @@
+Samtools implements various utilities for post-processing alignments in the
+SAM, BAM, and CRAM formats, including indexing, variant calling (in conjunction
+with bcftools), and a simple alignment viewer.
+
+WWW: http://www.htslib.org/
diff --git a/biology/samtools/pkg-plist b/biology/samtools/pkg-plist
new file mode 100644
index 000000000000..a708d0c3390f
--- /dev/null
+++ b/biology/samtools/pkg-plist
@@ -0,0 +1,22 @@
+bin/samtools
+bin/samtools_misc/ace2sam
+bin/samtools_misc/blast2sam.pl
+bin/samtools_misc/bowtie2sam.pl
+bin/samtools_misc/export2sam.pl
+bin/samtools_misc/interpolate_sam.pl
+bin/samtools_misc/maq2sam-long
+bin/samtools_misc/maq2sam-short
+bin/samtools_misc/md5fa
+bin/samtools_misc/md5sum-lite
+bin/samtools_misc/novo2sam.pl
+bin/samtools_misc/plot-bamstats
+bin/samtools_misc/psl2sam.pl
+bin/samtools_misc/sam2vcf.pl
+bin/samtools_misc/samtools.pl
+bin/samtools_misc/seq_cache_populate.pl
+bin/samtools_misc/soap2sam.pl
+bin/samtools_misc/varfilter.py
+bin/samtools_misc/wgsim
+bin/samtools_misc/wgsim_eval.pl
+bin/samtools_misc/zoom2sam.pl
+man/man1/samtools.1.gz