path: root/var/spack/repos/builtin/packages/bcftools/makefile_13.patch

--- 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