Cnvnator: a new package. (#8959)

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)