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Update and fix bcftools package (#14505)

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* 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 2020-01-14 22:04:47 -06:00 committed by Adam J. Stewart
parent e78f3ed040
commit 9f6ac938b7
6 changed files with 372 additions and 1 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

16
var/spack/repos/builtin/packages/bcftools/fix_mk.patch Normal file
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@ -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)

13
var/spack/repos/builtin/packages/bcftools/guess-ploidy.py_2to3.patch Normal file
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@ -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]

109
var/spack/repos/builtin/packages/bcftools/makefile_12.patch Normal file
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@ -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

102
var/spack/repos/builtin/packages/bcftools/makefile_13.patch Normal file
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@ -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

64
var/spack/repos/builtin/packages/bcftools/makefile_14.patch Normal file
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@ -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

69
var/spack/repos/builtin/packages/bcftools/package.py
View File

@ -4,6 +4,7 @@
# SPDX-License-Identifier: (Apache-2.0 OR MIT) # SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import * from spack import *
import glob
class Bcftools(AutotoolsPackage): class Bcftools(AutotoolsPackage):
@ -15,6 +16,7 @@ class Bcftools(AutotoolsPackage):
homepage = "http://samtools.github.io/bcftools/" homepage = "http://samtools.github.io/bcftools/"
url = "https://github.com/samtools/bcftools/releases/download/1.3.1/bcftools-1.3.1.tar.bz2" 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('1.9', sha256='6f36d0e6f16ec4acf88649fb1565d443acf0ba40f25a9afd87f14d14d13070c8')
version('1.8', sha256='4acbfd691f137742e0be63d09f516434f0faf617a5c60f466140e0677915fced') version('1.8', sha256='4acbfd691f137742e0be63d09f516434f0faf617a5c60f466140e0677915fced')
version('1.7', sha256='dd4f63d91b0dffb0f0ce88ac75c2387251930c8063f7799611265083f8d302d1') version('1.7', sha256='dd4f63d91b0dffb0f0ce88ac75c2387251930c8063f7799611265083f8d302d1')
@ -23,8 +25,22 @@ class Bcftools(AutotoolsPackage):
version('1.3.1', sha256='12c37a4054cbf1980223e2b3a80a7fdb3fd850324a4ba6832e38fdba91f1b924') version('1.3.1', sha256='12c37a4054cbf1980223e2b3a80a7fdb3fd850324a4ba6832e38fdba91f1b924')
version('1.2', sha256='53c628339020dd45334a007c9cefdaf1cba3f1032492ec813b116379fa684fd6') 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@1.9', when='@1.9')
depends_on('htslib@1.8', when='@1.8') depends_on('htslib@1.8', when='@1.8')
depends_on('htslib@1.7', when='@1.7') 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@1.3.1', when='@1.3.1')
depends_on('htslib@1.2', when='@1.2') 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): def configure_args(self):
args = [] args = []
args.append('--with-htslib={0}'.format(self.spec['htslib'].prefix)) 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 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)