Update and fix bcftools package (#14505)
* Update and fix bcftools package This PR updates bcftools to 1.10.2 and is dependent on PR #14504. This PR also fixes builds of other versions. Versions 1.2-1.4 did not use autotools so when the packaeg was converted to use autotools with version 1.6 those older versions could no longer build. Also, those versions needed to be patched to use an external htsllib. The method of finding the external htslib is also different for those older versions. In addition, this PR adds two variants to bcftools: - libgsl - perl-filters Finally, dependencies for perl and python are added, and an unused dependency for libzip was removed. * Do not use '@' in variant description The '@' character in a variant description will cause a problem with `spack info`. ``` ==> Error: Incomplete color format: '@' in expressions, for @1.8: ``` * Fix error with python2 processing this package
This commit is contained in:
Glenn Johnson
Adam J. Stewart
parent
e78f3ed040
commit
9f6ac938b7
6 changed files with 372 additions and 1 deletions
16
var/spack/repos/builtin/packages/bcftools/fix_mk.patch
Normal file
16
var/spack/repos/builtin/packages/bcftools/fix_mk.patch
Normal file
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@ -0,0 +1,16 @@
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diff -ru a/plugins/fixploidy.mk b/plugins/fixploidy.mk
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--- a/plugins/fixploidy.mk 2014-10-09 04:01:22.000000000 -0500
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+++ b/plugins/fixploidy.mk 2020-01-13 21:55:28.926309796 -0600
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@@ -1,2 +1,2 @@
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-plugins/fixploidy.so: plugins/fixploidy.c version.h version.c ploidy.h ploidy.c $(HTSDIR)/libhts.so
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- $(CC) $(CFLAGS) $(INCLUDES) -fPIC -shared -o $@ ploidy.c version.c $< -L$(HTSDIR) -lhts
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+plugins/fixploidy.so: plugins/fixploidy.c version.h version.c ploidy.h ploidy.c
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+ $(CC) $(CFLAGS) $(INCLUDES) -fPIC -shared -o $@ ploidy.c version.c $< $(HTSLIB)
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diff -ru a/plugins/vcf2sex.mk b/plugins/vcf2sex.mk
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--- a/plugins/vcf2sex.mk 2014-10-09 04:01:22.000000000 -0500
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+++ b/plugins/vcf2sex.mk 2020-01-13 21:55:55.056277406 -0600
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@@ -1,2 +1,2 @@
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-plugins/vcf2sex.so: plugins/vcf2sex.c version.h version.c ploidy.h ploidy.c $(HTSDIR)/libhts.so
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- $(CC) $(CFLAGS) $(INCLUDES) -fPIC -shared -o $@ ploidy.c version.c $< -L$(HTSDIR) -lhts
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+plugins/vcf2sex.so: plugins/vcf2sex.c version.h version.c ploidy.h ploidy.c
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+ $(CC) $(CFLAGS) $(INCLUDES) -fPIC -shared -o $@ ploidy.c version.c $< $(HTSLIB)
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@ -0,0 +1,13 @@
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--- a/misc/guess-ploidy.py 2017-04-07 04:52:44.000000000 -0500
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+++ b/misc/guess-ploidy.py 2020-01-14 10:59:49.738128654 -0600
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@@ -33,8 +33,8 @@
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csv.register_dialect('tab', delimiter='\t', quoting=csv.QUOTE_NONE)
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if len(sys.argv) != 3:
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- print >> sys.stderr, 'About: Plot output of "bcftools +guess-ploidy -v"'
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- print >> sys.stderr, 'Usage: guess-ploidy.py <guess-ploidy.out> <image-prefix>'
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+ print('About: Plot output of "bcftools +guess-ploidy -v"', file=sys.stderr)
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+ print('Usage: guess-ploidy.py <guess-ploidy.out> <image-prefix>', file=sys.stderr)
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sys.exit()
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prefix = sys.argv[2]
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109
var/spack/repos/builtin/packages/bcftools/makefile_12.patch
Normal file
109
var/spack/repos/builtin/packages/bcftools/makefile_12.patch
Normal file
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@ -0,0 +1,109 @@
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--- a/Makefile 2015-02-03 10:27:19.000000000 -0600
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+++ b/Makefile 2020-01-13 21:22:54.554904229 -0600
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@@ -30,10 +30,11 @@
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# Adjust $(HTSDIR) to point to your top-level htslib directory
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HTSDIR = htslib-1.2.1
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-include $(HTSDIR)/htslib.mk
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-HTSLIB = $(HTSDIR)/libhts.a
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-BGZIP = $(HTSDIR)/bgzip
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-TABIX = $(HTSDIR)/tabix
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+#include $(HTSDIR)/htslib.mk
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+HTSINC = $(HTSDIR)/include
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+HTSLIB = -L$(HTSDIR)/lib -lhts
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+BGZIP = $(HTSDIR)/bin/bgzip
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+TABIX = $(HTSDIR)/bin/tabix
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CC = gcc
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CFLAGS = -g -Wall -Wc++-compat -O2
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@@ -44,7 +45,7 @@
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vcfcall.o mcall.o vcmp.o gvcf.o reheader.o convert.o vcfconvert.o tsv2vcf.o \
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vcfcnv.o HMM.o vcfplugin.o consensus.o ploidy.o version.o \
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ccall.o em.o prob1.o kmin.o # the original samtools calling
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-INCLUDES = -I. -I$(HTSDIR)
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+INCLUDES = -I. -I$(HTSINC)
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# The polysomy command is not compiled by default because it brings dependency
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# on libgsl. The command can be compiled wth `make USE_GPL=1`. See the INSTALL
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@@ -52,7 +53,7 @@
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ifdef USE_GPL
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CFLAGS += -DUSE_GPL
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OBJS += polysomy.o
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- LDLIBS = -lgsl -lcblas
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+ LDLIBS = -lgsl -lgslcblas
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endif
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prefix = /usr/local
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@@ -102,8 +103,8 @@
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PLUGINS = $(PLUGINC:.c=.so)
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PLUGINM = $(PLUGINC:.c=.mk)
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-%.so: %.c version.h version.c $(HTSDIR)/libhts.so
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- $(CC) $(CFLAGS) $(INCLUDES) -fPIC -shared -o $@ version.c $< -L$(HTSDIR) -lhts
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+%.so: %.c version.h version.c
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+ $(CC) $(CFLAGS) $(INCLUDES) -fPIC -shared -o $@ version.c $< $(HTSLIB)
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-include $(PLUGINM)
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@@ -116,20 +117,20 @@
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tsv2vcf_h = tsv2vcf.h $(htslib_vcf_h)
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filter_h = filter.h $(htslib_vcf_h)
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prob1_h = prob1.h $(htslib_vcf_h) $(call_h)
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-roh_h = HMM.h $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(HTSDIR)/htslib/kstring.h $(HTSDIR)/htslib/kseq.h $(bcftools_h)
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+roh_h = HMM.h $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(HTSINC)/htslib/kstring.h $(HTSINC)/htslib/kseq.h $(bcftools_h)
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cnv_h = HMM.h $(htslib_vcf_h) $(htslib_synced_bcf_reader_h)
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main.o: main.c $(htslib_hts_h) version.h $(bcftools_h)
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-vcfannotate.o: vcfannotate.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(HTSDIR)/htslib/kseq.h $(bcftools_h) vcmp.h $(filter_h)
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-vcfplugin.o: vcfplugin.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(HTSDIR)/htslib/kseq.h $(bcftools_h) vcmp.h $(filter_h)
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-vcfcall.o: vcfcall.c $(htslib_vcf_h) $(HTSDIR)/htslib/kfunc.h $(htslib_synced_bcf_reader_h) $(bcftools_h) $(call_h) $(prob1_h)
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-vcfconcat.o: vcfconcat.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(HTSDIR)/htslib/kseq.h $(bcftools_h)
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+vcfannotate.o: vcfannotate.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(HTSINC)/htslib/kseq.h $(bcftools_h) vcmp.h $(filter_h)
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+vcfplugin.o: vcfplugin.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(HTSINC)/htslib/kseq.h $(bcftools_h) vcmp.h $(filter_h)
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+vcfcall.o: vcfcall.c $(htslib_vcf_h) $(HTSINC)/htslib/kfunc.h $(htslib_synced_bcf_reader_h) $(bcftools_h) $(call_h) $(prob1_h)
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+vcfconcat.o: vcfconcat.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(HTSINC)/htslib/kseq.h $(bcftools_h)
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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)
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vcffilter.o: vcffilter.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) $(filter_h) rbuf.h
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vcfgtcheck.o: vcfgtcheck.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h)
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vcfindex.o: vcfindex.c $(htslib_vcf_h) $(htslib_tbx_h)
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vcfisec.o: vcfisec.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) $(filter_h)
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-vcfmerge.o: vcfmerge.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) vcmp.h $(HTSDIR)/htslib/khash.h
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+vcfmerge.o: vcfmerge.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) vcmp.h $(HTSINC)/htslib/khash.h
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vcfnorm.o: vcfnorm.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_faidx_h) $(bcftools_h) rbuf.h
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vcfquery.o: vcfquery.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) $(filter_h) $(convert_h)
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vcfroh.o: vcfroh.c $(roh_h)
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@@ -137,20 +138,20 @@
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vcfsom.o: vcfsom.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h)
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vcfstats.o: vcfstats.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(htslib_faidx_h) $(bcftools_h)
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vcfview.o: vcfview.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) $(filter_h)
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-reheader.o: reheader.c $(htslib_vcf_h) $(htslib_bgzf_h) $(HTSDIR)/htslib/kseq.h $(bcftools_h)
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+reheader.o: reheader.c $(htslib_vcf_h) $(htslib_bgzf_h) $(HTSINC)/htslib/kseq.h $(bcftools_h)
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tabix.o: tabix.c $(htslib_bgzf_h) $(htslib_tbx_h)
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-ccall.o: ccall.c $(HTSDIR)/htslib/kfunc.h $(call_h) kmin.h $(prob1_h)
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+ccall.o: ccall.c $(HTSINC)/htslib/kfunc.h $(call_h) kmin.h $(prob1_h)
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convert.o: convert.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) $(convert_h)
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tsv2vcf.o: tsv2vcf.c $(tsv2vcf_h)
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em.o: em.c $(htslib_vcf_h) kmin.h $(call_h)
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-filter.o: filter.c $(HTSDIR)/htslib/khash_str2int.h $(filter_h) $(bcftools_h) $(htslib_hts_defs_h) $(htslib_vcfutils_h)
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+filter.o: filter.c $(HTSINC)/htslib/khash_str2int.h $(filter_h) $(bcftools_h) $(htslib_hts_defs_h) $(htslib_vcfutils_h)
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gvcf.o: gvcf.c $(call_h)
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kmin.o: kmin.c kmin.h
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-mcall.o: mcall.c $(HTSDIR)/htslib/kfunc.h $(call_h)
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+mcall.o: mcall.c $(HTSINC)/htslib/kfunc.h $(call_h)
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prob1.o: prob1.c $(prob1_h)
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vcmp.o: vcmp.c $(htslib_hts_h) vcmp.h
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polysomy.o: polysomy.c $(htslib_hts_h)
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-consensus.o: consensus.c $(htslib_hts_h) $(HTSDIR)/htslib/kseq.h rbuf.h $(bcftools_h) $(HTSDIR)/htslib/regidx.h
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+consensus.o: consensus.c $(htslib_hts_h) $(HTSINC)/htslib/kseq.h rbuf.h $(bcftools_h) $(HTSINC)/htslib/regidx.h
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version.o: version.h version.c
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test/test-rbuf.o: test/test-rbuf.c rbuf.h
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@@ -158,7 +159,7 @@
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test/test-rbuf: test/test-rbuf.o
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$(CC) $(CFLAGS) -o $@ -lm -ldl $<
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-bcftools: $(HTSLIB) $(OBJS)
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+bcftools: $(OBJS)
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$(CC) $(CFLAGS) -o $@ $(OBJS) $(HTSLIB) -lpthread -lz -lm -ldl $(LDLIBS)
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doc/bcftools.1: doc/bcftools.txt
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102
var/spack/repos/builtin/packages/bcftools/makefile_13.patch
Normal file
102
var/spack/repos/builtin/packages/bcftools/makefile_13.patch
Normal file
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@ -0,0 +1,102 @@
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--- a/Makefile 2016-10-02 21:23:39.289320362 -0500
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+++ b/Makefile 2016-10-02 21:30:41.163562704 -0500
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@@ -30,10 +30,11 @@
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# Adjust $(HTSDIR) to point to your top-level htslib directory
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HTSDIR = htslib-1.3.1
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-include $(HTSDIR)/htslib.mk
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-HTSLIB = $(HTSDIR)/libhts.a
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-BGZIP = $(HTSDIR)/bgzip
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-TABIX = $(HTSDIR)/tabix
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+#include $(HTSDIR)/htslib.mk
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+HTSINC = $(HTSDIR)/include
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+HTSLIB = -L$(HTSDIR)/lib -lhts
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+BGZIP = $(HTSDIR)/bin/bgzip
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+TABIX = $(HTSDIR)/bin/tabix
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CC = gcc
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CPPFLAGS =
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@@ -48,7 +49,7 @@
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vcfcnv.o HMM.o vcfplugin.o consensus.o ploidy.o version.o \
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ccall.o em.o prob1.o kmin.o # the original samtools calling
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-EXTRA_CPPFLAGS = -I. -I$(HTSDIR) -DPLUGINPATH=\"$(pluginpath)\"
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+EXTRA_CPPFLAGS = -I. -I$(HTSINC) -DPLUGINPATH=\"$(pluginpath)\"
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GSL_LIBS =
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# The polysomy command is not compiled by default because it brings dependency
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@@ -57,7 +58,7 @@
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ifdef USE_GPL
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EXTRA_CPPFLAGS += -DUSE_GPL
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OBJS += polysomy.o peakfit.o
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- GSL_LIBS = -lgsl -lcblas
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+ GSL_LIBS = -lgsl -lgslcblas
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endif
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prefix = /usr/local
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@@ -136,20 +137,20 @@
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filter_h = filter.h $(htslib_vcf_h)
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ploidy_h = ploidy.h $(htslib_regidx_h)
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prob1_h = prob1.h $(htslib_vcf_h) $(call_h)
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-roh_h = HMM.h $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(HTSDIR)/htslib/kstring.h $(HTSDIR)/htslib/kseq.h $(bcftools_h)
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+roh_h = HMM.h $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(HTSINC)/htslib/kstring.h $(HTSINC)/htslib/kseq.h $(bcftools_h)
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cnv_h = HMM.h $(htslib_vcf_h) $(htslib_synced_bcf_reader_h)
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main.o: main.c $(htslib_hts_h) version.h $(bcftools_h)
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-vcfannotate.o: vcfannotate.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(HTSDIR)/htslib/kseq.h $(bcftools_h) vcmp.h $(filter_h)
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-vcfplugin.o: vcfplugin.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(HTSDIR)/htslib/kseq.h $(bcftools_h) vcmp.h $(filter_h)
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-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)
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-vcfconcat.o: vcfconcat.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(HTSDIR)/htslib/kseq.h $(htslib_bgzf_h) $(htslib_tbx_h) $(bcftools_h)
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+vcfannotate.o: vcfannotate.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(HTSINC)/htslib/kseq.h $(bcftools_h) vcmp.h $(filter_h)
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+vcfplugin.o: vcfplugin.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(HTSINC)/htslib/kseq.h $(bcftools_h) vcmp.h $(filter_h)
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+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)
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+vcfconcat.o: vcfconcat.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(HTSINC)/htslib/kseq.h $(htslib_bgzf_h) $(htslib_tbx_h) $(bcftools_h)
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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)
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vcffilter.o: vcffilter.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) $(filter_h) rbuf.h
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vcfgtcheck.o: vcfgtcheck.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h)
|
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vcfindex.o: vcfindex.c $(htslib_vcf_h) $(htslib_tbx_h)
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vcfisec.o: vcfisec.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) $(filter_h)
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-vcfmerge.o: vcfmerge.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) vcmp.h $(HTSDIR)/htslib/khash.h
|
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+vcfmerge.o: vcfmerge.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) vcmp.h $(HTSINC)/htslib/khash.h
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vcfnorm.o: vcfnorm.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_faidx_h) $(bcftools_h) rbuf.h
|
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vcfquery.o: vcfquery.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) $(filter_h) $(convert_h)
|
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vcfroh.o: vcfroh.c $(roh_h)
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@@ -157,22 +158,22 @@
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vcfsom.o: vcfsom.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h)
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vcfstats.o: vcfstats.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(htslib_faidx_h) $(bcftools_h)
|
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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
|
||||
64
var/spack/repos/builtin/packages/bcftools/makefile_14.patch
Normal file
64
var/spack/repos/builtin/packages/bcftools/makefile_14.patch
Normal file
|
|
@ -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
|
||||
|
|
@ -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)
|
||||
|
|
|
|||
Loading…
Reference in a new issue