Index: head/biology/bcftools/Makefile =================================================================== --- head/biology/bcftools/Makefile (revision 476246) +++ head/biology/bcftools/Makefile (revision 476247) @@ -1,52 +1,65 @@ # Created by: Reed A. Cartwright # $FreeBSD$ PORTNAME= bcftools -PORTVERSION= 1.6 -PORTREVISION= 1 +PORTVERSION= 1.9 CATEGORIES= biology MAINTAINER= cartwright@asu.edu COMMENT= Tools for manipulating next-generation sequencing data LICENSE= MIT -# LICENSE_FILE= ${WRKSRC}/LICENSE +LICENSE_FILE= ${WRKSRC}/LICENSE BUILD_DEPENDS= htslib>=1.6:biology/htslib LIB_DEPENDS= libhts.so:biology/htslib TEST_DEPENDS= bash:shells/bash CONFLICTS_BUILD=openssl +USES= autoreconf gmake localbase \ + perl5 python:env shebangfix + USE_GITHUB= yes GH_ACCOUNT= samtools -USES= autoreconf gmake perl5 python:env shebangfix +USE_LDCONFIG= ${PREFIX}/libexec/${PORTNAME} USE_PERL5= test GNU_CONFIGURE= yes -SUB_FILES= pkg-message SHEBANG_FILES= misc/* test/test.pl OPTIONS_DEFINE= GPL GPL_DESC= Enable modules that rely on GPL code OPTIONS_DEFAULT= GPL GPL_LIB_DEPENDS= libgsl.so:math/gsl .include -CPPFLAGS+= -I${LOCALBASE}/include -LDFLAGS+= -L${LOCALBASE}/lib - .if ${PORT_OPTIONS:MGPL} MAKE_ENV+= USE_GPL=1 -LICENSE= GPLv3 +LICENSE+= GPLv3 +LICENSE_COMB= multi .endif TEST_TARGET= test post-patch: - @${GREP} -q '@PORTVERSION@' ${WRKSRC}/configure.ac || (echo "@PORTVERSION@ in file/patch-configure.ac is overwritten probably due to using 'make makepatch'"; exit 1) @${REINPLACE_CMD} -e 's|@PORTVERSION@|${PORTVERSION}|g' ${WRKSRC}/configure.ac + +post-install: + ${MV} ${STAGEDIR}${PREFIX}/bin/samtools_misc/color-chrs.pl \ + ${STAGEDIR}${PREFIX}/bin/color-chrs + ${MV} ${STAGEDIR}${PREFIX}/bin/samtools_misc/guess-ploidy.py\ + ${STAGEDIR}${PREFIX}/bin/guess-ploidy + ${MV} /${STAGEDIR}${PREFIX}/bin/samtools_misc/plot-roh.py \ + ${STAGEDIR}${PREFIX}/bin/plot-roh + ${MV} ${STAGEDIR}${PREFIX}/bin/samtools_misc/run-roh.pl \ + ${STAGEDIR}${PREFIX}/bin/run-roh + ${MV} ${STAGEDIR}${PREFIX}/bin/samtools_misc/vcfutils.pl \ + ${STAGEDIR}${PREFIX}/bin/vcfutils + ${MV} ${STAGEDIR}${PREFIX}/bin/samtools_misc/plot-vcfstats \ + ${STAGEDIR}${PREFIX}/bin/ + ${RMDIR} ${STAGEDIR}${PREFIX}/bin/samtools_misc/ .include Index: head/biology/bcftools/distinfo =================================================================== --- head/biology/bcftools/distinfo (revision 476246) +++ head/biology/bcftools/distinfo (revision 476247) @@ -1,3 +1,3 @@ -TIMESTAMP = 1508307708 -SHA256 (samtools-bcftools-1.6_GH0.tar.gz) = afb2a96d3419fbe77fab5c501dc28bc5e691145353ac5600909a75c0e625f025 -SIZE (samtools-bcftools-1.6_GH0.tar.gz) = 2333330 +TIMESTAMP = 1532903716 +SHA256 (samtools-bcftools-1.9_GH0.tar.gz) = 223b90c9a9b11576174384de70abe8e8394aef1b45c7324e4bf875d0f344e96e +SIZE (samtools-bcftools-1.9_GH0.tar.gz) = 2394968 Index: head/biology/bcftools/files/patch-Makefile =================================================================== --- head/biology/bcftools/files/patch-Makefile (revision 476246) +++ head/biology/bcftools/files/patch-Makefile (revision 476247) @@ -1,79 +1,79 @@ ---- Makefile.orig 2017-09-28 11:22:48 UTC +--- Makefile.orig 2018-07-18 08:34:29 UTC +++ Makefile @@ -22,10 +22,10 @@ # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER # DEALINGS IN THE SOFTWARE. -CC = gcc -CPPFLAGS = -CFLAGS = -g -Wall -Wc++-compat -O2 -LDFLAGS = +CC ?= cc +CPPFLAGS += +CFLAGS += -Wall +LDFLAGS += LIBS = DYNAMIC_FLAGS = -rdynamic @@ -42,26 +42,25 @@ OBJS = main.o vcfindex.o tabix.o \ vcfsort.o \ ccall.o em.o prob1.o kmin.o # the original samtools calling -prefix = /usr/local +prefix = ${PREFIX} exec_prefix = $(prefix) bindir = $(exec_prefix)/bin libdir = $(exec_prefix)/lib libexecdir = $(exec_prefix)/libexec -mandir = $(prefix)/share/man +mandir = $(prefix)/man man1dir = $(mandir)/man1 # Installation location for $(PLUGINS) plugindir = $(libexecdir)/bcftools pluginpath = $(plugindir) # Installation location for $(MISC_PROGRAMS) and $(MISC_SCRIPTS) -misc_bindir = $(bindir) +misc_bindir = $(bindir)/samtools_misc MKDIR_P = mkdir -p -INSTALL = install -p -INSTALL_DATA = $(INSTALL) -m 644 -INSTALL_DIR = $(MKDIR_P) -m 755 -INSTALL_MAN = $(INSTALL_DATA) -INSTALL_PROGRAM = $(INSTALL) -INSTALL_SCRIPT = $(INSTALL_PROGRAM) +INSTALL_DATA = ${BSD_INSTALL_DATA} +INSTALL_DIR = $(MKDIR_P) +INSTALL_MAN = ${BSD_INSTALL_MAN} +INSTALL_PROGRAM = ${BSD_INSTALL_PROGRAM} +INSTALL_SCRIPT = ${BSD_INSTALL_SCRIPT} PROGRAMS = bcftools MISC_SCRIPTS = \ @@ -77,7 +76,7 @@ all: $(PROGRAMS) $(TEST_PROGRAMS) plugin ALL_CPPFLAGS = -I. $(HTSLIB_CPPFLAGS) $(CPPFLAGS) ALL_LDFLAGS = $(HTSLIB_LDFLAGS) $(LDFLAGS) -ALL_LIBS = -lz -ldl $(LIBS) +ALL_LIBS = -lz $(LIBS) # Usually config.mk and config.h are generated by running configure # or config.status, but if those aren't used create defaults here. @@ -131,7 +130,7 @@ print-version: ifdef USE_GPL main.o : EXTRA_CPPFLAGS += -DUSE_GPL OBJS += polysomy.o peakfit.o - GSL_LIBS ?= -lgsl -lcblas + GSL_LIBS ?= -lgsl -lgslcblas endif bcftools: $(OBJS) $(HTSLIB) -@@ -273,7 +272,7 @@ docs: doc/bcftools.1 doc/bcftools.html +@@ -278,7 +277,7 @@ docs: doc/bcftools.1 doc/bcftools.html # Since there is no make dependency, bcftools.1 can be out-of-date and # make docs can be run to update if asciidoc is available - install: $(PROG) $(PLUGINS) + install: $(PROGRAMS) $(PLUGINS) - $(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(man1dir) $(DESTDIR)$(plugindir) + $(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(misc_bindir) $(DESTDIR)$(man1dir) $(DESTDIR)$(plugindir) $(INSTALL_PROGRAM) $(PROGRAMS) $(DESTDIR)$(bindir) $(INSTALL_SCRIPT) $(MISC_SCRIPTS) $(DESTDIR)$(misc_bindir) $(INSTALL_MAN) doc/bcftools.1 $(DESTDIR)$(man1dir) Index: head/biology/bcftools/files/patch-configure.ac =================================================================== --- head/biology/bcftools/files/patch-configure.ac (revision 476246) +++ head/biology/bcftools/files/patch-configure.ac (revision 476247) @@ -1,11 +1,11 @@ ---- configure.ac.orig 2017-09-28 11:22:48 UTC +--- configure.ac.orig 2018-07-18 08:34:29 UTC +++ configure.ac @@ -23,7 +23,7 @@ # DEALINGS IN THE SOFTWARE. dnl Process this file with autoconf to produce a configure script --AC_INIT([BCFtools], m4_esyscmd_s([make print-version]), +-AC_INIT([BCFtools], m4_esyscmd_s([./version.sh 2>/dev/null]), +AC_INIT([BCFtools], [@PORTVERSION@], [samtools-help@lists.sourceforge.net], [], [http://www.htslib.org/]) AC_PREREQ([2.63]) dnl This version introduced 4-argument AC_CHECK_HEADER AC_CONFIG_SRCDIR([main.c]) Index: head/biology/bcftools/pkg-plist =================================================================== --- head/biology/bcftools/pkg-plist (revision 476246) +++ head/biology/bcftools/pkg-plist (revision 476247) @@ -1,32 +1,36 @@ bin/bcftools -bin/samtools_misc/color-chrs.pl -bin/samtools_misc/guess-ploidy.py -bin/samtools_misc/plot-roh.py -bin/samtools_misc/plot-vcfstats -bin/samtools_misc/run-roh.pl -bin/samtools_misc/vcfutils.pl +bin/color-chrs +bin/guess-ploidy +bin/plot-roh +bin/plot-vcfstats +bin/run-roh +bin/vcfutils libexec/bcftools/GTisec.so libexec/bcftools/GTsubset.so libexec/bcftools/ad-bias.so libexec/bcftools/af-dist.so libexec/bcftools/check-ploidy.so libexec/bcftools/check-sparsity.so libexec/bcftools/color-chrs.so +libexec/bcftools/contrast.so libexec/bcftools/counts.so libexec/bcftools/dosage.so libexec/bcftools/fill-AN-AC.so libexec/bcftools/fill-from-fasta.so libexec/bcftools/fill-tags.so libexec/bcftools/fixploidy.so libexec/bcftools/fixref.so libexec/bcftools/frameshifts.so libexec/bcftools/guess-ploidy.so libexec/bcftools/impute-info.so libexec/bcftools/isecGT.so libexec/bcftools/mendelian.so libexec/bcftools/missing2ref.so libexec/bcftools/prune.so libexec/bcftools/setGT.so +libexec/bcftools/smpl-stats.so +libexec/bcftools/split.so libexec/bcftools/tag2tag.so +libexec/bcftools/trio-stats.so libexec/bcftools/trio-switch-rate.so man/man1/bcftools.1.gz