Date: Sun, 14 Dec 2014 22:35:08 +0000 (UTC) From: Pawel Pekala <pawel@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r374729 - in head/biology: . htslib htslib/files Message-ID: <201412142235.sBEMZ8CQ047767@svn.freebsd.org>
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Author: pawel Date: Sun Dec 14 22:35:07 2014 New Revision: 374729 URL: https://svnweb.freebsd.org/changeset/ports/374729 QAT: https://qat.redports.org/buildarchive/r374729/ Log: 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> Added: head/biology/htslib/ head/biology/htslib/Makefile (contents, props changed) head/biology/htslib/distinfo (contents, props changed) head/biology/htslib/files/ head/biology/htslib/files/patch-Makefile (contents, props changed) head/biology/htslib/pkg-descr (contents, props changed) head/biology/htslib/pkg-plist (contents, props changed) Modified: head/biology/Makefile Modified: head/biology/Makefile ============================================================================== --- head/biology/Makefile Sun Dec 14 22:17:23 2014 (r374728) +++ head/biology/Makefile Sun Dec 14 22:35:07 2014 (r374729) @@ -26,6 +26,7 @@ SUBDIR += gperiodic SUBDIR += grappa SUBDIR += hmmer + SUBDIR += htslib SUBDIR += iolib SUBDIR += jalview SUBDIR += lagan Added: head/biology/htslib/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/htslib/Makefile Sun Dec 14 22:35:07 2014 (r374729) @@ -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> Added: head/biology/htslib/distinfo ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/htslib/distinfo Sun Dec 14 22:35:07 2014 (r374729) @@ -0,0 +1,2 @@ +SHA256 (htslib-1.1.tar.gz) = 0614de1795284181675dd0178fb00f0aca176064b6263e3c7e21b53f34710631 +SIZE (htslib-1.1.tar.gz) = 957434 Added: head/biology/htslib/files/patch-Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/htslib/files/patch-Makefile Sun Dec 14 22:35:07 2014 (r374729) @@ -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) + Added: head/biology/htslib/pkg-descr ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/htslib/pkg-descr Sun Dec 14 22:35:07 2014 (r374729) @@ -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/ Added: head/biology/htslib/pkg-plist ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/htslib/pkg-plist Sun Dec 14 22:35:07 2014 (r374729) @@ -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
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