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-rw-r--r--var/spack/repos/builtin/packages/cnvnator/package.py50
1 files changed, 50 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/cnvnator/package.py b/var/spack/repos/builtin/packages/cnvnator/package.py
new file mode 100644
index 0000000000..42216cf324
--- /dev/null
+++ b/var/spack/repos/builtin/packages/cnvnator/package.py
@@ -0,0 +1,50 @@
+# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Cnvnator(MakefilePackage):
+ """A tool for CNV discovery and genotyping
+ from depth-of-coverage by mapped reads."""
+
+ homepage = "https://github.com/abyzovlab/CNVnator"
+ url = "https://github.com/abyzovlab/CNVnator/archive/v0.3.3.tar.gz"
+
+ version('0.3.3', 'f9fc0c2e79abe85decab00d3748d8904')
+
+ depends_on('samtools')
+ depends_on('htslib')
+ depends_on('root')
+ depends_on('bzip2')
+ depends_on('curl')
+ depends_on('lzma')
+ depends_on('zlib')
+
+ def edit(self, spec, prefix):
+ makefile = FileFilter('Makefile')
+ # Replace -fopenmp with self.compiler.openmp_flag
+ makefile.filter('-fopenmp', self.compiler.openmp_flag)
+ # Replace CXX with CXXFLAGS
+ makefile.filter('CXX.*=.*',
+ r'CXXFLAGS = -DCNVNATOR_VERSION=\"$(VERSION)\"'
+ ' $(OMPFLAGS)'
+ ' {0}'.format(self.compiler.cxx11_flag))
+ makefile.filter('$(CXX)', '$(CXX) $(CXXFLAGS)', string=True)
+ # Replace -I$(SAMDIR) with -I$(SAMINC)
+ makefile.filter('-I$(SAMDIR)', '-I$(SAMINC)', string=True)
+ # Link more libs
+ makefile.filter('^override LIBS.*',
+ 'override LIBS += -lz -lbz2 -lcurl -llzma')
+
+ def build(self, spec, prefix):
+ make('ROOTSYS={0}'.format(spec['root'].prefix),
+ 'SAMINC={0}'.format(spec['samtools'].prefix.include),
+ 'SAMDIR={0}'.format(spec['samtools'].prefix.lib),
+ 'HTSDIR={0}'.format(spec['htslib'].prefix.lib))
+
+ def install(self, spec, prefix):
+ mkdir(prefix.bin)
+ install('cnvnator', prefix.bin)