From owner-svn-ports-all@FreeBSD.ORG Fri Jun 5 21:01:16 2015 Return-Path: Delivered-To: svn-ports-all@freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2001:1900:2254:206a::19:1]) (using TLSv1.2 with cipher AECDH-AES256-SHA (256/256 bits)) (No client certificate requested) by hub.freebsd.org (Postfix) with ESMTPS id EC35FC87; Fri, 5 Jun 2015 21:01:16 +0000 (UTC) (envelope-from pi@FreeBSD.org) Received: from svn.freebsd.org (svn.freebsd.org [IPv6:2001:1900:2254:2068::e6a:0]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (Client did not present a certificate) by mx1.freebsd.org (Postfix) with ESMTPS id D99841EB1; Fri, 5 Jun 2015 21:01:16 +0000 (UTC) (envelope-from pi@FreeBSD.org) Received: from svn.freebsd.org ([127.0.1.70]) by svn.freebsd.org (8.14.9/8.14.9) with ESMTP id t55L1G6p044782; Fri, 5 Jun 2015 21:01:16 GMT (envelope-from pi@FreeBSD.org) Received: (from pi@localhost) by svn.freebsd.org (8.14.9/8.14.9/Submit) id t55L1EvM044761; Fri, 5 Jun 2015 21:01:14 GMT (envelope-from pi@FreeBSD.org) Message-Id: <201506052101.t55L1EvM044761@svn.freebsd.org> X-Authentication-Warning: svn.freebsd.org: pi set sender to pi@FreeBSD.org using -f From: Kurt Jaeger Date: Fri, 5 Jun 2015 21:01:14 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r388638 - in head/biology: . bcftools bcftools/files X-SVN-Group: ports-head MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-BeenThere: svn-ports-all@freebsd.org X-Mailman-Version: 2.1.20 Precedence: list List-Id: SVN commit messages for the ports tree List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Fri, 05 Jun 2015 21:01:17 -0000 Author: pi Date: Fri Jun 5 21:01:13 2015 New Revision: 388638 URL: https://svnweb.freebsd.org/changeset/ports/388638 Log: 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 Added: head/biology/bcftools/ head/biology/bcftools/Makefile (contents, props changed) head/biology/bcftools/distinfo (contents, props changed) head/biology/bcftools/files/ head/biology/bcftools/files/patch-Makefile (contents, props changed) head/biology/bcftools/files/patch-plugins_fixploidy.mk (contents, props changed) head/biology/bcftools/files/patch-plugins_vcf2sex.mk (contents, props changed) head/biology/bcftools/files/patch-prob1.c (contents, props changed) head/biology/bcftools/files/pkg-message.in (contents, props changed) head/biology/bcftools/pkg-descr (contents, props changed) head/biology/bcftools/pkg-plist (contents, props changed) Modified: head/biology/Makefile Modified: head/biology/Makefile ============================================================================== --- head/biology/Makefile Fri Jun 5 20:39:57 2015 (r388637) +++ head/biology/Makefile Fri Jun 5 21:01:13 2015 (r388638) @@ -7,6 +7,7 @@ SUBDIR += artemis SUBDIR += avida SUBDIR += babel + SUBDIR += bcftools SUBDIR += biococoa SUBDIR += biojava SUBDIR += blat Added: head/biology/bcftools/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/bcftools/Makefile Fri Jun 5 21:01:13 2015 (r388638) @@ -0,0 +1,48 @@ +# Created by: Reed A. Cartwright +# $FreeBSD$ + +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 + +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 Added: head/biology/bcftools/distinfo ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/bcftools/distinfo Fri Jun 5 21:01:13 2015 (r388638) @@ -0,0 +1,2 @@ +SHA256 (samtools-bcftools-1.2_GH0.tar.gz) = 90ccd7dccfb0b2848b71f32fff073c420260e857b7feeb89c1fb4bfaba49bfba +SIZE (samtools-bcftools-1.2_GH0.tar.gz) = 511625 Added: head/biology/bcftools/files/patch-Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/bcftools/files/patch-Makefile Fri Jun 5 21:01:13 2015 (r388638) @@ -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 Added: head/biology/bcftools/files/patch-plugins_fixploidy.mk ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/bcftools/files/patch-plugins_fixploidy.mk Fri Jun 5 21:01:13 2015 (r388638) @@ -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 Added: head/biology/bcftools/files/patch-plugins_vcf2sex.mk ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/bcftools/files/patch-plugins_vcf2sex.mk Fri Jun 5 21:01:13 2015 (r388638) @@ -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 Added: head/biology/bcftools/files/patch-prob1.c ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/bcftools/files/patch-prob1.c Fri Jun 5 21:01:13 2015 (r388638) @@ -0,0 +1,17 @@ +--- prob1.c.orig 2015-04-28 01:28:23 UTC ++++ prob1.c +@@ -33,6 +33,14 @@ THE SOFTWARE. */ + #include + #include "prob1.h" + ++#include ++#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) Added: head/biology/bcftools/files/pkg-message.in ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/bcftools/files/pkg-message.in Fri Jun 5 21:01:13 2015 (r388638) @@ -0,0 +1,2 @@ + +Add %%PREFIX%%/bin/samtools_misc to your path to use miscellaneous tools. Added: head/biology/bcftools/pkg-descr ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/bcftools/pkg-descr Fri Jun 5 21:01:13 2015 (r388638) @@ -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/ Added: head/biology/bcftools/pkg-plist ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/bcftools/pkg-plist Fri Jun 5 21:01:13 2015 (r388638) @@ -0,0 +1,4 @@ +bin/bcftools +bin/samtools_misc/plot-vcfstats +bin/samtools_misc/vcfutils.pl +man/man1/bcftools.1.gz