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7c0aee41271b5a59fca2ce4849de21f25c402d1a
spack/var/spack/repos/builtin/packages/bcftools/makefile_12.patch

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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
2020-01-14 22:04:47 -06:00
--- 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
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