diff options
6 files changed, 372 insertions, 1 deletions
diff --git a/var/spack/repos/builtin/packages/bcftools/fix_mk.patch b/var/spack/repos/builtin/packages/bcftools/fix_mk.patch new file mode 100644 index 0000000000..0625138ac8 --- /dev/null +++ b/var/spack/repos/builtin/packages/bcftools/fix_mk.patch @@ -0,0 +1,16 @@ +diff -ru a/plugins/fixploidy.mk b/plugins/fixploidy.mk +--- a/plugins/fixploidy.mk 2014-10-09 04:01:22.000000000 -0500 ++++ b/plugins/fixploidy.mk 2020-01-13 21:55:28.926309796 -0600 +@@ -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) $(INCLUDES) -fPIC -shared -o $@ ploidy.c version.c $< $(HTSLIB) +diff -ru a/plugins/vcf2sex.mk b/plugins/vcf2sex.mk +--- a/plugins/vcf2sex.mk 2014-10-09 04:01:22.000000000 -0500 ++++ b/plugins/vcf2sex.mk 2020-01-13 21:55:55.056277406 -0600 +@@ -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) $(INCLUDES) -fPIC -shared -o $@ ploidy.c version.c $< $(HTSLIB) diff --git a/var/spack/repos/builtin/packages/bcftools/guess-ploidy.py_2to3.patch b/var/spack/repos/builtin/packages/bcftools/guess-ploidy.py_2to3.patch new file mode 100644 index 0000000000..68918a547e --- /dev/null +++ b/var/spack/repos/builtin/packages/bcftools/guess-ploidy.py_2to3.patch @@ -0,0 +1,13 @@ +--- a/misc/guess-ploidy.py 2017-04-07 04:52:44.000000000 -0500 ++++ b/misc/guess-ploidy.py 2020-01-14 10:59:49.738128654 -0600 +@@ -33,8 +33,8 @@ + csv.register_dialect('tab', delimiter='\t', quoting=csv.QUOTE_NONE) + + if len(sys.argv) != 3: +- print >> sys.stderr, 'About: Plot output of "bcftools +guess-ploidy -v"' +- print >> sys.stderr, 'Usage: guess-ploidy.py <guess-ploidy.out> <image-prefix>' ++ print('About: Plot output of "bcftools +guess-ploidy -v"', file=sys.stderr) ++ print('Usage: guess-ploidy.py <guess-ploidy.out> <image-prefix>', file=sys.stderr) + sys.exit() + + prefix = sys.argv[2] diff --git a/var/spack/repos/builtin/packages/bcftools/makefile_12.patch b/var/spack/repos/builtin/packages/bcftools/makefile_12.patch new file mode 100644 index 0000000000..1083a0dce9 --- /dev/null +++ b/var/spack/repos/builtin/packages/bcftools/makefile_12.patch @@ -0,0 +1,109 @@ +--- a/Makefile 2015-02-03 10:27:19.000000000 -0600 ++++ b/Makefile 2020-01-13 21:22:54.554904229 -0600 +@@ -30,10 +30,11 @@ + + # Adjust $(HTSDIR) to point to your top-level htslib directory + HTSDIR = htslib-1.2.1 +-include $(HTSDIR)/htslib.mk +-HTSLIB = $(HTSDIR)/libhts.a +-BGZIP = $(HTSDIR)/bgzip +-TABIX = $(HTSDIR)/tabix ++#include $(HTSDIR)/htslib.mk ++HTSINC = $(HTSDIR)/include ++HTSLIB = -L$(HTSDIR)/lib -lhts ++BGZIP = $(HTSDIR)/bin/bgzip ++TABIX = $(HTSDIR)/bin/tabix + + CC = gcc + CFLAGS = -g -Wall -Wc++-compat -O2 +@@ -44,7 +45,7 @@ + vcfcall.o mcall.o vcmp.o gvcf.o reheader.o convert.o vcfconvert.o tsv2vcf.o \ + vcfcnv.o HMM.o vcfplugin.o consensus.o ploidy.o version.o \ + ccall.o em.o prob1.o kmin.o # the original samtools calling +-INCLUDES = -I. -I$(HTSDIR) ++INCLUDES = -I. -I$(HTSINC) + + # The polysomy command is not compiled by default because it brings dependency + # on libgsl. The command can be compiled wth `make USE_GPL=1`. See the INSTALL +@@ -52,7 +53,7 @@ + ifdef USE_GPL + CFLAGS += -DUSE_GPL + OBJS += polysomy.o +- LDLIBS = -lgsl -lcblas ++ LDLIBS = -lgsl -lgslcblas + endif + + prefix = /usr/local +@@ -102,8 +103,8 @@ + 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) $(INCLUDES) -fPIC -shared -o $@ version.c $< $(HTSLIB) + + -include $(PLUGINM) + +@@ -116,20 +117,20 @@ + tsv2vcf_h = tsv2vcf.h $(htslib_vcf_h) + filter_h = filter.h $(htslib_vcf_h) + prob1_h = prob1.h $(htslib_vcf_h) $(call_h) +-roh_h = HMM.h $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(HTSDIR)/htslib/kstring.h $(HTSDIR)/htslib/kseq.h $(bcftools_h) ++roh_h = HMM.h $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(HTSINC)/htslib/kstring.h $(HTSINC)/htslib/kseq.h $(bcftools_h) + cnv_h = HMM.h $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) + + main.o: main.c $(htslib_hts_h) version.h $(bcftools_h) +-vcfannotate.o: vcfannotate.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(HTSDIR)/htslib/kseq.h $(bcftools_h) vcmp.h $(filter_h) +-vcfplugin.o: vcfplugin.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(HTSDIR)/htslib/kseq.h $(bcftools_h) vcmp.h $(filter_h) +-vcfcall.o: vcfcall.c $(htslib_vcf_h) $(HTSDIR)/htslib/kfunc.h $(htslib_synced_bcf_reader_h) $(bcftools_h) $(call_h) $(prob1_h) +-vcfconcat.o: vcfconcat.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(HTSDIR)/htslib/kseq.h $(bcftools_h) ++vcfannotate.o: vcfannotate.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(HTSINC)/htslib/kseq.h $(bcftools_h) vcmp.h $(filter_h) ++vcfplugin.o: vcfplugin.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(HTSINC)/htslib/kseq.h $(bcftools_h) vcmp.h $(filter_h) ++vcfcall.o: vcfcall.c $(htslib_vcf_h) $(HTSINC)/htslib/kfunc.h $(htslib_synced_bcf_reader_h) $(bcftools_h) $(call_h) $(prob1_h) ++vcfconcat.o: vcfconcat.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(HTSINC)/htslib/kseq.h $(bcftools_h) + vcfconvert.o: vcfconvert.c $(htslib_vcf_h) $(htslib_bgzf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) $(filter_h) $(convert_h) $(tsv2vcf_h) + vcffilter.o: vcffilter.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) $(filter_h) rbuf.h + vcfgtcheck.o: vcfgtcheck.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) + vcfindex.o: vcfindex.c $(htslib_vcf_h) $(htslib_tbx_h) + vcfisec.o: vcfisec.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) $(filter_h) +-vcfmerge.o: vcfmerge.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) vcmp.h $(HTSDIR)/htslib/khash.h ++vcfmerge.o: vcfmerge.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) vcmp.h $(HTSINC)/htslib/khash.h + vcfnorm.o: vcfnorm.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_faidx_h) $(bcftools_h) rbuf.h + vcfquery.o: vcfquery.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) $(filter_h) $(convert_h) + vcfroh.o: vcfroh.c $(roh_h) +@@ -137,20 +138,20 @@ + vcfsom.o: vcfsom.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) + vcfstats.o: vcfstats.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(htslib_faidx_h) $(bcftools_h) + vcfview.o: vcfview.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) $(filter_h) +-reheader.o: reheader.c $(htslib_vcf_h) $(htslib_bgzf_h) $(HTSDIR)/htslib/kseq.h $(bcftools_h) ++reheader.o: reheader.c $(htslib_vcf_h) $(htslib_bgzf_h) $(HTSINC)/htslib/kseq.h $(bcftools_h) + tabix.o: tabix.c $(htslib_bgzf_h) $(htslib_tbx_h) +-ccall.o: ccall.c $(HTSDIR)/htslib/kfunc.h $(call_h) kmin.h $(prob1_h) ++ccall.o: ccall.c $(HTSINC)/htslib/kfunc.h $(call_h) kmin.h $(prob1_h) + convert.o: convert.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) $(convert_h) + tsv2vcf.o: tsv2vcf.c $(tsv2vcf_h) + em.o: em.c $(htslib_vcf_h) kmin.h $(call_h) +-filter.o: filter.c $(HTSDIR)/htslib/khash_str2int.h $(filter_h) $(bcftools_h) $(htslib_hts_defs_h) $(htslib_vcfutils_h) ++filter.o: filter.c $(HTSINC)/htslib/khash_str2int.h $(filter_h) $(bcftools_h) $(htslib_hts_defs_h) $(htslib_vcfutils_h) + gvcf.o: gvcf.c $(call_h) + kmin.o: kmin.c kmin.h +-mcall.o: mcall.c $(HTSDIR)/htslib/kfunc.h $(call_h) ++mcall.o: mcall.c $(HTSINC)/htslib/kfunc.h $(call_h) + prob1.o: prob1.c $(prob1_h) + vcmp.o: vcmp.c $(htslib_hts_h) vcmp.h + polysomy.o: polysomy.c $(htslib_hts_h) +-consensus.o: consensus.c $(htslib_hts_h) $(HTSDIR)/htslib/kseq.h rbuf.h $(bcftools_h) $(HTSDIR)/htslib/regidx.h ++consensus.o: consensus.c $(htslib_hts_h) $(HTSINC)/htslib/kseq.h rbuf.h $(bcftools_h) $(HTSINC)/htslib/regidx.h + version.o: version.h version.c + + test/test-rbuf.o: test/test-rbuf.c rbuf.h +@@ -158,7 +159,7 @@ + test/test-rbuf: test/test-rbuf.o + $(CC) $(CFLAGS) -o $@ -lm -ldl $< + +-bcftools: $(HTSLIB) $(OBJS) ++bcftools: $(OBJS) + $(CC) $(CFLAGS) -o $@ $(OBJS) $(HTSLIB) -lpthread -lz -lm -ldl $(LDLIBS) + + doc/bcftools.1: doc/bcftools.txt diff --git a/var/spack/repos/builtin/packages/bcftools/makefile_13.patch b/var/spack/repos/builtin/packages/bcftools/makefile_13.patch new file mode 100644 index 0000000000..5be31ed2ca --- /dev/null +++ b/var/spack/repos/builtin/packages/bcftools/makefile_13.patch @@ -0,0 +1,102 @@ +--- a/Makefile 2016-10-02 21:23:39.289320362 -0500 ++++ b/Makefile 2016-10-02 21:30:41.163562704 -0500 +@@ -30,10 +30,11 @@ + + # Adjust $(HTSDIR) to point to your top-level htslib directory + HTSDIR = htslib-1.3.1 +-include $(HTSDIR)/htslib.mk +-HTSLIB = $(HTSDIR)/libhts.a +-BGZIP = $(HTSDIR)/bgzip +-TABIX = $(HTSDIR)/tabix ++#include $(HTSDIR)/htslib.mk ++HTSINC = $(HTSDIR)/include ++HTSLIB = -L$(HTSDIR)/lib -lhts ++BGZIP = $(HTSDIR)/bin/bgzip ++TABIX = $(HTSDIR)/bin/tabix + + CC = gcc + CPPFLAGS = +@@ -48,7 +49,7 @@ + vcfcnv.o HMM.o vcfplugin.o consensus.o ploidy.o version.o \ + ccall.o em.o prob1.o kmin.o # the original samtools calling + +-EXTRA_CPPFLAGS = -I. -I$(HTSDIR) -DPLUGINPATH=\"$(pluginpath)\" ++EXTRA_CPPFLAGS = -I. -I$(HTSINC) -DPLUGINPATH=\"$(pluginpath)\" + GSL_LIBS = + + # The polysomy command is not compiled by default because it brings dependency +@@ -57,7 +58,7 @@ + ifdef USE_GPL + EXTRA_CPPFLAGS += -DUSE_GPL + OBJS += polysomy.o peakfit.o +- GSL_LIBS = -lgsl -lcblas ++ GSL_LIBS = -lgsl -lgslcblas + endif + + prefix = /usr/local +@@ -136,20 +137,20 @@ + filter_h = filter.h $(htslib_vcf_h) + ploidy_h = ploidy.h $(htslib_regidx_h) + prob1_h = prob1.h $(htslib_vcf_h) $(call_h) +-roh_h = HMM.h $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(HTSDIR)/htslib/kstring.h $(HTSDIR)/htslib/kseq.h $(bcftools_h) ++roh_h = HMM.h $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(HTSINC)/htslib/kstring.h $(HTSINC)/htslib/kseq.h $(bcftools_h) + cnv_h = HMM.h $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) + + main.o: main.c $(htslib_hts_h) version.h $(bcftools_h) +-vcfannotate.o: vcfannotate.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(HTSDIR)/htslib/kseq.h $(bcftools_h) vcmp.h $(filter_h) +-vcfplugin.o: vcfplugin.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(HTSDIR)/htslib/kseq.h $(bcftools_h) vcmp.h $(filter_h) +-vcfcall.o: vcfcall.c $(htslib_vcf_h) $(HTSDIR)/htslib/kfunc.h $(htslib_synced_bcf_reader_h) $(HTSDIR)/htslib/khash_str2int.h $(bcftools_h) $(call_h) $(prob1_h) $(ploidy_h) +-vcfconcat.o: vcfconcat.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(HTSDIR)/htslib/kseq.h $(htslib_bgzf_h) $(htslib_tbx_h) $(bcftools_h) ++vcfannotate.o: vcfannotate.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(HTSINC)/htslib/kseq.h $(bcftools_h) vcmp.h $(filter_h) ++vcfplugin.o: vcfplugin.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(HTSINC)/htslib/kseq.h $(bcftools_h) vcmp.h $(filter_h) ++vcfcall.o: vcfcall.c $(htslib_vcf_h) $(HTSINC)/htslib/kfunc.h $(htslib_synced_bcf_reader_h) $(HTSINC)/htslib/khash_str2int.h $(bcftools_h) $(call_h) $(prob1_h) $(ploidy_h) ++vcfconcat.o: vcfconcat.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(HTSINC)/htslib/kseq.h $(htslib_bgzf_h) $(htslib_tbx_h) $(bcftools_h) + vcfconvert.o: vcfconvert.c $(htslib_vcf_h) $(htslib_bgzf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) $(filter_h) $(convert_h) $(tsv2vcf_h) + vcffilter.o: vcffilter.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) $(filter_h) rbuf.h + vcfgtcheck.o: vcfgtcheck.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) + vcfindex.o: vcfindex.c $(htslib_vcf_h) $(htslib_tbx_h) + vcfisec.o: vcfisec.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) $(filter_h) +-vcfmerge.o: vcfmerge.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) vcmp.h $(HTSDIR)/htslib/khash.h ++vcfmerge.o: vcfmerge.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) vcmp.h $(HTSINC)/htslib/khash.h + vcfnorm.o: vcfnorm.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_faidx_h) $(bcftools_h) rbuf.h + vcfquery.o: vcfquery.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) $(filter_h) $(convert_h) + vcfroh.o: vcfroh.c $(roh_h) +@@ -157,22 +158,22 @@ + vcfsom.o: vcfsom.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) + vcfstats.o: vcfstats.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(htslib_faidx_h) $(bcftools_h) + vcfview.o: vcfview.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) $(filter_h) +-reheader.o: reheader.c $(htslib_vcf_h) $(htslib_bgzf_h) $(htslib_tbx_h) $(HTSDIR)/htslib/kseq.h $(bcftools_h) ++reheader.o: reheader.c $(htslib_vcf_h) $(htslib_bgzf_h) $(htslib_tbx_h) $(HTSINC)/htslib/kseq.h $(bcftools_h) + tabix.o: tabix.c $(htslib_bgzf_h) $(htslib_tbx_h) +-ccall.o: ccall.c $(HTSDIR)/htslib/kfunc.h $(call_h) kmin.h $(prob1_h) ++ccall.o: ccall.c $(HTSINC)/htslib/kfunc.h $(call_h) kmin.h $(prob1_h) + convert.o: convert.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) $(convert_h) + tsv2vcf.o: tsv2vcf.c $(tsv2vcf_h) + em.o: em.c $(htslib_vcf_h) kmin.h $(call_h) +-filter.o: filter.c $(HTSDIR)/htslib/khash_str2int.h $(filter_h) $(bcftools_h) $(htslib_hts_defs_h) $(htslib_vcfutils_h) ++filter.o: filter.c $(HTSINC)/htslib/khash_str2int.h $(filter_h) $(bcftools_h) $(htslib_hts_defs_h) $(htslib_vcfutils_h) + gvcf.o: gvcf.c $(call_h) + kmin.o: kmin.c kmin.h +-mcall.o: mcall.c $(HTSDIR)/htslib/kfunc.h $(call_h) ++mcall.o: mcall.c $(HTSINC)/htslib/kfunc.h $(call_h) + prob1.o: prob1.c $(prob1_h) + vcmp.o: vcmp.c $(htslib_hts_h) vcmp.h +-ploidy.o: ploidy.c $(htslib_regidx_h) $(HTSDIR)/htslib/khash_str2int.h $(HTSDIR)/htslib/kseq.h $(htslib_hts_h) $(bcftools_h) $(ploidy_h) ++ploidy.o: ploidy.c $(htslib_regidx_h) $(HTSINC)/htslib/khash_str2int.h $(HTSINC)/htslib/kseq.h $(htslib_hts_h) $(bcftools_h) $(ploidy_h) + polysomy.o: polysomy.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(bcftools_h) peakfit.h +-peakfit.o: peakfit.c peakfit.h $(htslib_hts_h) $(HTSDIR)/htslib/kstring.h +-consensus.o: consensus.c $(htslib_hts_h) $(HTSDIR)/htslib/kseq.h rbuf.h $(bcftools_h) $(HTSDIR)/htslib/regidx.h ++peakfit.o: peakfit.c peakfit.h $(htslib_hts_h) $(HTSINC)/htslib/kstring.h ++consensus.o: consensus.c $(htslib_hts_h) $(HTSINC)/htslib/kseq.h rbuf.h $(bcftools_h) $(HTSINC)/htslib/regidx.h + version.o: version.h version.c + + test/test-rbuf.o: test/test-rbuf.c rbuf.h +@@ -180,7 +181,7 @@ + test/test-rbuf: test/test-rbuf.o + $(CC) $(LDFLAGS) -o $@ $^ -lm $(LIBS) + +-bcftools: $(HTSLIB) $(OBJS) ++bcftools: $(OBJS) + $(CC) -rdynamic $(LDFLAGS) -o $@ $(OBJS) $(HTSLIB) -lpthread -lz -lm -ldl $(GSL_LIBS) $(LIBS) + + doc/bcftools.1: doc/bcftools.txt diff --git a/var/spack/repos/builtin/packages/bcftools/makefile_14.patch b/var/spack/repos/builtin/packages/bcftools/makefile_14.patch new file mode 100644 index 0000000000..fe780cf8f7 --- /dev/null +++ b/var/spack/repos/builtin/packages/bcftools/makefile_14.patch @@ -0,0 +1,64 @@ +--- a/Makefile 2017-03-13 09:55:48.000000000 -0500 ++++ b/Makefile 2020-01-13 17:42:49.359554802 -0600 +@@ -30,13 +30,14 @@ + + # Adjust $(HTSDIR) to point to your top-level htslib directory + HTSDIR = htslib-1.4 +-include $(HTSDIR)/htslib.mk +-include $(HTSDIR)/htslib_static.mk +-HTSLIB = $(HTSDIR)/libhts.a +-BGZIP = $(HTSDIR)/bgzip +-TABIX = $(HTSDIR)/tabix +-HTSLIB_LDFLAGS = $(HTSLIB_static_LDFLAGS) +-HTSLIB_LIBS = $(HTSLIB_static_LIBS) ++#include $(HTSDIR)/htslib.mk ++#include $(HTSDIR)/htslib_static.mk ++HTSINC = $(HTSDIR)/include ++HTSLIB = -L$(HTSDIR)/lib -lhts ++BGZIP = $(HTSDIR)/bin/bgzip ++TABIX = $(HTSDIR)/bin/tabix ++#HTSLIB_LDFLAGS = $(HTSLIB_static_LDFLAGS) ++#HTSLIB_LIBS = $(HTSLIB_static_LIBS) + + CC = gcc + CPPFLAGS = +@@ -51,7 +52,7 @@ + endif + + # TODO Use configure or htslib.pc to add -rdynamic/-ldl conditionally +-ALL_CPPFLAGS = -I. $(HTSLIB_CPPFLAGS) $(CPPFLAGS) ++ALL_CPPFLAGS = -I. -I$(HTSINC) + ALL_LDFLAGS = $(DYNAMIC_FLAGS) $(HTSLIB_LDFLAGS) $(LDFLAGS) + ALL_LIBS = -lm -lz -ldl $(LIBS) + +@@ -64,7 +65,7 @@ + mpileup.o bam2bcf.o bam2bcf_indel.o bam_sample.o \ + ccall.o em.o prob1.o kmin.o # the original samtools calling + +-EXTRA_CPPFLAGS = -I. -I$(HTSDIR) -DPLUGINPATH=\"$(pluginpath)\" ++EXTRA_CPPFLAGS = -I. -I$(HTSINC) -DPLUGINPATH=\"$(pluginpath)\" + GSL_LIBS = + + # The polysomy command is not compiled by default because it brings dependency +@@ -73,7 +74,7 @@ + ifdef USE_GPL + EXTRA_CPPFLAGS += -DUSE_GPL + OBJS += polysomy.o peakfit.o +- GSL_LIBS = -lgsl -lcblas ++ GSL_LIBS = -lgsl -lgslcblas + endif + + prefix = /usr/local +@@ -208,10 +209,10 @@ + + test/test-regidx.o: test/test-regidx.c regidx.h + +-test/test-regidx: test/test-regidx.o regidx.o $(HTSLIB) ++test/test-regidx: test/test-regidx.o regidx.o + $(CC) $(ALL_LDFLAGS) -o $@ $^ $(HTSLIB) -lpthread $(HTSLIB_LIBS) $(ALL_LIBS) + +-bcftools: $(HTSLIB) $(OBJS) ++bcftools: $(OBJS) + $(CC) $(ALL_LDFLAGS) -o $@ $(OBJS) $(HTSLIB) -lpthread $(HTSLIB_LIBS) $(GSL_LIBS) $(ALL_LIBS) + + doc/bcftools.1: doc/bcftools.txt diff --git a/var/spack/repos/builtin/packages/bcftools/package.py b/var/spack/repos/builtin/packages/bcftools/package.py index 1fd1a34da9..28f431e346 100644 --- a/var/spack/repos/builtin/packages/bcftools/package.py +++ b/var/spack/repos/builtin/packages/bcftools/package.py @@ -4,6 +4,7 @@ # SPDX-License-Identifier: (Apache-2.0 OR MIT) from spack import * +import glob class Bcftools(AutotoolsPackage): @@ -15,6 +16,7 @@ class Bcftools(AutotoolsPackage): homepage = "http://samtools.github.io/bcftools/" url = "https://github.com/samtools/bcftools/releases/download/1.3.1/bcftools-1.3.1.tar.bz2" + version('1.10.2', sha256='f57301869d0055ce3b8e26d8ad880c0c1989bf25eaec8ea5db99b60e31354e2c') version('1.9', sha256='6f36d0e6f16ec4acf88649fb1565d443acf0ba40f25a9afd87f14d14d13070c8') version('1.8', sha256='4acbfd691f137742e0be63d09f516434f0faf617a5c60f466140e0677915fced') version('1.7', sha256='dd4f63d91b0dffb0f0ce88ac75c2387251930c8063f7799611265083f8d302d1') @@ -23,8 +25,22 @@ class Bcftools(AutotoolsPackage): version('1.3.1', sha256='12c37a4054cbf1980223e2b3a80a7fdb3fd850324a4ba6832e38fdba91f1b924') version('1.2', sha256='53c628339020dd45334a007c9cefdaf1cba3f1032492ec813b116379fa684fd6') - depends_on('libzip', when='@1.8:') + variant('libgsl', + default=False, + description='build options that require the GNU scientific ' + 'library') + variant('perl-filters', + default=False, + description='build in support for PERL scripts in -i/-e ' + 'filtering expressions, for versions >= 1.8.') + + depends_on('gsl', when='+libgsl') + depends_on('py-matplotlib', when='@1.6:', type='run') + depends_on('perl', when='@1.8:~perl-filters', type='run') + depends_on('perl', when='@1.8:+perl-filters', type=('build', 'run')) + + depends_on('htslib@1.10.2', when='@1.10.2') depends_on('htslib@1.9', when='@1.9') depends_on('htslib@1.8', when='@1.8') depends_on('htslib@1.7', when='@1.7') @@ -33,8 +49,59 @@ class Bcftools(AutotoolsPackage): depends_on('htslib@1.3.1', when='@1.3.1') depends_on('htslib@1.2', when='@1.2') + patch('makefile_12.patch', when='@1.2') + patch('fix_mk.patch', when='@1.2') + patch('makefile_13.patch', when='@1.3') + patch('makefile_14.patch', when='@1.4') + patch('guess-ploidy.py_2to3.patch', when='@1.6:1.9') + + @when('@1.5:') def configure_args(self): args = [] + args.append('--with-htslib={0}'.format(self.spec['htslib'].prefix)) + args.extend(self.enable_or_disable('libgsl')) + + if self.spec.satisfies('@1.8:'): + args.extend(self.enable_or_disable('perl-filters')) return args + + @when('@1.2:1.4') + def set_make_options(self): + options = [] + + options.append('prefix={0}'.format(self.prefix)) + options.append('HTSDIR={0}'.format(self.spec['htslib'].prefix)) + + if '+libgsl' in self.spec: + options.append('USE_GPL=1') + + return options + + @when('@1.2:1.4') + def autoreconf(self, spec, prefix): + touch('configure') + + @when('@1.2:1.4') + def configure(self, spec, prefix): + pass + + @when('@1.2:1.4') + def build(self, spec, prefix): + make_options = self.set_make_options() + make(*make_options) + + @when('@1.2:1.4') + def install(self, spec, prefix): + make_options = self.set_make_options() + make('install', *make_options) + + if spec.satisfies('@1.2'): + mkdirp(self.prefix.libexec.bcftools) + for files in glob.glob('plugins/*.so'): + install(files, self.prefix.libexec.bcftools) + + @when('@1.2') + def setup_run_environment(self, env): + env.set('BCFTOOLS_PLUGINS', self.prefix.libexec.bcftools) |