strelka: new package (#5632)

* Add package for strelka@2.8.2

* Fix flake8 complaints

1 files changed, 88 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/strelka/package.py b/var/spack/repos/builtin/packages/strelka/package.py
new file mode 100644
index 0000000000..5c3da7c635
--- /dev/null
+++ b/var/spack/repos/builtin/packages/strelka/package.py
@@ -0,0 +1,88 @@
+##############################################################################
+# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Strelka(CMakePackage):
+    """Somatic and germline small variant caller for mapped sequencing
+       data."""
+
+    homepage = "https://github.com/Illumina/strelka"
+    url      = "https://github.com/Illumina/strelka/releases/download/v2.8.2/strelka-2.8.2.release_src.tar.bz2"
+
+    version('2.8.2', 'c48753997fcf2e4edac4e9854495721e')
+
+    depends_on('python@2.4:')
+    depends_on('zlib')
+    depends_on('bzip2')
+    depends_on('cmake@2.8.5:')
+    depends_on('boost@1.56.0')
+
+    @run_before('install')
+    def filter_sbang(self):
+        """Run before install so that the standard Spack sbang install hook
+           can fix up the path to the python binary.
+        """
+
+        match = '^#!/usr/bin/env python'
+        python = self.spec['python'].command
+        substitute = "#!{p}".format(p=python)
+        kwargs = {'ignore_absent': False, 'backup': False, 'string': False}
+        with working_dir('src'):
+            files = [
+                'config/validate/validateJsonModelFromSchema.py',
+                'srcqc/run_cppcheck.py',
+                'python/libexec/cat.py',
+                'python/libexec/sortVcf.py',
+                'python/libexec/extractSmallIndelCandidates.py',
+                'python/libexec/configureStrelkaNoiseWorkflow.py',
+                'python/libexec/configureSequenceErrorCountsWorkflow.py',
+                'python/libexec/vcfCmdlineSwapper.py',
+                'python/libexec/mergeChromDepth.py',
+                'python/scoringModelTraining/germline/bin/evs_learn.py',
+                'python/scoringModelTraining/germline/bin/parseAnnotatedTrainingVcf.py',  # noqa: E501
+                'python/scoringModelTraining/germline/bin/filterTrainingVcf.py',  # noqa: E501
+                'python/scoringModelTraining/germline/bin/evs_exportmodel.py',
+                'python/scoringModelTraining/germline/bin/evs_qq.py',
+                'python/scoringModelTraining/germline/bin/evs_pr.py',
+                'python/scoringModelTraining/germline/bin/evs_evaluate.py',
+                'python/scoringModelTraining/somatic/bin/evs_random_sample_tpfp.py',  # noqa: E501
+                'python/scoringModelTraining/somatic/bin/evs_learn.py',
+                'python/scoringModelTraining/somatic/bin/evs_random_split_csv.py',  # noqa: E501
+                'python/scoringModelTraining/somatic/bin/vcf_to_feature_csv.py',  # noqa: E501
+                'python/scoringModelTraining/somatic/bin/calc_features.py',
+                'python/scoringModelTraining/somatic/bin/evs_exportmodel.py',
+                'python/scoringModelTraining/somatic/bin/evs_pr.py',
+                'python/scoringModelTraining/somatic/bin/evs_evaluate.py',
+                'python/bin/configureStrelkaGermlineWorkflow.py',
+                'python/bin/configureStrelkaSomaticWorkflow.py',
+            ]
+            filter_file(match, substitute, *files, **kwargs)
+
+        with working_dir('spack-build/redist'):
+            files = [
+                'pyflow-1.1.18/src/pyflow.py',
+            ]
+            filter_file(match, substitute, *files, **kwargs)