From 9f6ac938b71c920e93c3c26a015d4b2dc13d7517 Mon Sep 17 00:00:00 2001
From: Glenn Johnson <glenn-johnson@uiowa.edu>
Date: Tue, 14 Jan 2020 22:04:47 -0600
Subject: [PATCH] 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
---
.../builtin/packages/bcftools/fix_mk.patch | 16 +++
.../bcftools/guess-ploidy.py_2to3.patch | 13 +++
.../packages/bcftools/makefile_12.patch | 109 ++++++++++++++++++
.../packages/bcftools/makefile_13.patch | 102 ++++++++++++++++
.../packages/bcftools/makefile_14.patch | 64 ++++++++++
.../builtin/packages/bcftools/package.py | 69 ++++++++++-
6 files changed, 372 insertions(+), 1 deletion(-)
create mode 100644 var/spack/repos/builtin/packages/bcftools/fix_mk.patch
create mode 100644 var/spack/repos/builtin/packages/bcftools/guess-ploidy.py_2to3.patch
create mode 100644 var/spack/repos/builtin/packages/bcftools/makefile_12.patch
create mode 100644 var/spack/repos/builtin/packages/bcftools/makefile_13.patch
create mode 100644 var/spack/repos/builtin/packages/bcftools/makefile_14.patch
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)
--
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