HTSlib is an implementation of a unified C library for accessing common file

formats, such as SAM, CRAM, VCF, and BCF, used for high-throughput sequencing
data. It is the core library used by samtools and bcftools.

WWW: http://www.htslib.org/

PR:		195591
Submitted by:	Reed A. Cartwright <cartwright@asu.edu>

5 files changed, 130 insertions, 0 deletions

diff --git a/biology/htslib/Makefile b/biology/htslib/Makefile
new file mode 100644
index 000000000000..b5abcfaecaac
--- /dev/null
+++ b/biology/htslib/Makefile
@@ -0,0 +1,29 @@
+# Created by: Reed A. Cartwright <cartwright@asu.edu>
+# $FreeBSD$
+
+PORTNAME=	htslib
+PORTVERSION=	1.1
+CATEGORIES=	biology devel
+
+MAINTAINER=	cartwright@asu.edu
+COMMENT=	C library for high-throughput sequencing data formats
+
+LICENSE=	BSD3CLAUSE MIT
+LICENSE_COMB=	multi
+LICENSE_FILE=	${WRKSRC}/LICENSE
+
+USE_GITHUB=	yes
+GH_ACCOUNT=	samtools
+GH_COMMIT=	a65fba2
+
+USES=		gmake
+USE_LDCONFIG=	yes
+
+MAKE_ENV=	INSTALL_LIB="${INSTALL_LIB}" \
+		INSTALL_DATA="${INSTALL_DATA}" \
+		INSTALL_PROGRAM="${INSTALL_PROGRAM}" \
+		INSTALL_DIR="${MKDIR}"
+
+PLIST_SUB=	PORTVERSION="${PORTVERSION}"
+
+.include <bsd.port.mk>
diff --git a/biology/htslib/distinfo b/biology/htslib/distinfo
new file mode 100644
index 000000000000..ca1b3fd93d6c
--- /dev/null
+++ b/biology/htslib/distinfo
@@ -0,0 +1,2 @@
+SHA256 (htslib-1.1.tar.gz) = 0614de1795284181675dd0178fb00f0aca176064b6263e3c7e21b53f34710631
+SIZE (htslib-1.1.tar.gz) = 957434
diff --git a/biology/htslib/files/patch-Makefile b/biology/htslib/files/patch-Makefile
new file mode 100644
index 000000000000..5a1b1e3300a9
--- /dev/null
+++ b/biology/htslib/files/patch-Makefile
@@ -0,0 +1,64 @@
+--- Makefile.orig	2014-09-23 14:39:41 UTC
++++ Makefile
+@@ -22,33 +22,27 @@
+ # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+ # DEALINGS IN THE SOFTWARE.
+ 
+-CC     = gcc
+-AR     = ar
+-RANLIB = ranlib
++CC    ?= cc
++AR     = /usr/bin/ar
++RANLIB = /usr/bin/ranlib
+ 
+ # TODO: edit cram code to remove need for -DSAMTOOLS
+-CPPFLAGS = -I. -DSAMTOOLS=1
++CPPFLAGS += -I. -DSAMTOOLS=1 -Wno-unused-function -Wno-implicit-function-declaration
+ # TODO: probably update cram code to make it compile cleanly with -Wc++-compat
+-CFLAGS   = -g -Wall -O2
++CFLAGS   += -Wall
+ EXTRA_CFLAGS_PIC = -fpic
+-LDFLAGS  =
+-LDLIBS   =
++LDFLAGS  +=
++LDLIBS   +=
+ 
+-prefix      = /usr/local
++prefix      = ${STAGEDIR}${PREFIX}
+ exec_prefix = $(prefix)
+ bindir      = $(exec_prefix)/bin
+ includedir  = $(prefix)/include
+ libdir      = $(exec_prefix)/lib
+-mandir      = $(prefix)/share/man
++mandir      = $(prefix)/man
+ man1dir     = $(mandir)/man1
+ man5dir     = $(mandir)/man5
+-pkgconfigdir= $(libdir)/pkgconfig
+-
+-MKDIR_P = mkdir -p
+-INSTALL = install -p
+-INSTALL_PROGRAM = $(INSTALL)
+-INSTALL_DATA    = $(INSTALL) -m 644
+-INSTALL_DIR     = $(MKDIR_P) -m 755
++pkgconfigdir= $(exec_prefix)/libdata/pkgconfig
+ 
+ BUILT_PROGRAMS = \
+ 	bgzip \
+@@ -62,7 +56,7 @@ BUILT_TEST_PROGRAMS = \
+ 	test/test-vcf-api \
+ 	test/test-vcf-sweep
+ 
+-all: lib-static lib-shared $(BUILT_PROGRAMS) $(BUILT_TEST_PROGRAMS)
++all: lib-static lib-shared $(BUILT_PROGRAMS)
+ 
+ HTSPREFIX =
+ include htslib_vars.mk
+@@ -284,7 +278,7 @@ installdirs:
+ # and libhts.so.NN (used by client executables at runtime).
+ 
+ install-so: libhts.so installdirs
+-	$(INSTALL_DATA) libhts.so $(DESTDIR)$(libdir)/libhts.so.$(PACKAGE_VERSION)
++	$(INSTALL_LIB) libhts.so $(DESTDIR)$(libdir)/libhts.so.$(PACKAGE_VERSION)
+ 	ln -sf libhts.so.$(PACKAGE_VERSION) $(DESTDIR)$(libdir)/libhts.so
+ 	ln -sf libhts.so.$(PACKAGE_VERSION) $(DESTDIR)$(libdir)/libhts.so.$(LIBHTS_SOVERSION)
+ 
diff --git a/biology/htslib/pkg-descr b/biology/htslib/pkg-descr
new file mode 100644
index 000000000000..4abab85879ac
--- /dev/null
+++ b/biology/htslib/pkg-descr
@@ -0,0 +1,5 @@
+HTSlib is an implementation of a unified C library for accessing common file
+formats, such as SAM, CRAM, VCF, and BCF, used for high-throughput sequencing
+data. It is the core library used by samtools and bcftools.
+
+WWW: http://www.htslib.org/
diff --git a/biology/htslib/pkg-plist b/biology/htslib/pkg-plist
new file mode 100644
index 000000000000..74ec1c18ac77
--- /dev/null
+++ b/biology/htslib/pkg-plist
@@ -0,0 +1,30 @@
+bin/bgzip
+bin/tabix
+include/htslib/bgzf.h
+include/htslib/faidx.h
+include/htslib/hfile.h
+include/htslib/hts.h
+include/htslib/hts_defs.h
+include/htslib/kfunc.h
+include/htslib/khash.h
+include/htslib/khash_str2int.h
+include/htslib/klist.h
+include/htslib/knetfile.h
+include/htslib/kseq.h
+include/htslib/ksort.h
+include/htslib/kstring.h
+include/htslib/sam.h
+include/htslib/synced_bcf_reader.h
+include/htslib/tbx.h
+include/htslib/vcf.h
+include/htslib/vcf_sweep.h
+include/htslib/vcfutils.h
+lib/libhts.a
+lib/libhts.so
+lib/libhts.so.1
+lib/libhts.so.%%PORTVERSION%%
+libdata/pkgconfig/htslib.pc
+man/man1/tabix.1.gz
+man/man5/faidx.5.gz
+man/man5/sam.5.gz
+man/man5/vcf.5.gz