Date: Mon, 15 Dec 2014 21:59:20 +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: r374767 - in head/biology: . samtools samtools/files Message-ID: <201412152159.sBFLxK1Z031819@svn.freebsd.org>
next in thread | raw e-mail | index | archive | help
Author: pawel Date: Mon Dec 15 21:59:19 2014 New Revision: 374767 URL: https://svnweb.freebsd.org/changeset/ports/374767 QAT: https://qat.redports.org/buildarchive/r374767/ Log: 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/ PR: 195592 Submitted by: Reed A. Cartwright <cartwright@asu.edu> Added: head/biology/samtools/ head/biology/samtools/Makefile (contents, props changed) head/biology/samtools/distinfo (contents, props changed) head/biology/samtools/files/ head/biology/samtools/files/patch-Makefile (contents, props changed) head/biology/samtools/files/patch-errmod.c (contents, props changed) head/biology/samtools/files/pkg-message.in (contents, props changed) head/biology/samtools/pkg-descr (contents, props changed) head/biology/samtools/pkg-plist (contents, props changed) Modified: head/biology/Makefile Modified: head/biology/Makefile ============================================================================== --- head/biology/Makefile Mon Dec 15 21:44:59 2014 (r374766) +++ head/biology/Makefile Mon Dec 15 21:59:19 2014 (r374767) @@ -76,6 +76,7 @@ SUBDIR += python-nexus SUBDIR += recombine SUBDIR += ruby-bio + SUBDIR += samtools SUBDIR += seaview SUBDIR += seqan SUBDIR += seqio Added: head/biology/samtools/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/samtools/Makefile Mon Dec 15 21:59:19 2014 (r374767) @@ -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> Added: head/biology/samtools/distinfo ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/samtools/distinfo Mon Dec 15 21:59:19 2014 (r374767) @@ -0,0 +1,2 @@ +SHA256 (samtools-1.1.tar.gz) = adf674bef85e6ffd88d19178a46f229fc033c7302610d5a51ef9709dd0346c59 +SIZE (samtools-1.1.tar.gz) = 4321336 Added: head/biology/samtools/files/patch-Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/samtools/files/patch-Makefile Mon Dec 15 21:59:19 2014 (r374767) @@ -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) + + Added: head/biology/samtools/files/patch-errmod.c ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/samtools/files/patch-errmod.c Mon Dec 15 21:59:19 2014 (r374767) @@ -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) Added: head/biology/samtools/files/pkg-message.in ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/samtools/files/pkg-message.in Mon Dec 15 21:59:19 2014 (r374767) @@ -0,0 +1,2 @@ + +Add %%PREFIX%%/bin/samtools_misc to your path to use miscellaneous tools. Added: head/biology/samtools/pkg-descr ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/samtools/pkg-descr Mon Dec 15 21:59:19 2014 (r374767) @@ -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/ Added: head/biology/samtools/pkg-plist ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/samtools/pkg-plist Mon Dec 15 21:59:19 2014 (r374767) @@ -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
Want to link to this message? Use this URL: <https://mail-archive.FreeBSD.org/cgi/mid.cgi?201412152159.sBFLxK1Z031819>