From ab2c7573c19da142b1aaccbff6c2863cdc46d337 Mon Sep 17 00:00:00 2001
From: George Hartzell <hartzell@alerce.com>
Date: Mon, 9 Oct 2017 16:02:44 -0700
Subject: strelka: new package (#5632)
* Add package for strelka@2.8.2
* Fix flake8 complaints
---
.../repos/builtin/packages/strelka/package.py | 88 ++++++++++++++++++++++
1 file changed, 88 insertions(+)
create mode 100644 var/spack/repos/builtin/packages/strelka/package.py
(limited to 'var')
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)
--
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