delly2: new package (#5820)

var/spack/repos/builtin/packages/delly2/package.py

@@ -0,0 +1,65 @@
+##############################################################################
+# 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 Delly2(MakefilePackage):
+    """Delly2 is an integrated structural variant prediction method that can
+       discover, genotype and visualize deletions, tandem duplications,
+       inversions and translocations at single-nucleotide resolution in
+       short-read massively parallel sequencing data.."""
+
+    homepage = "https://github.com/dellytools/delly"
+    url      = "https://github.com/dellytools/delly"
+
+    version('2017-08-03', commit='e32a9cd55c7e3df5a6ae4a91f31a0deb354529fc',
+            git='https://github.com/dellytools/delly.git')
+
+    depends_on('htslib')
+    depends_on('boost')
+    depends_on('bcftools')
+
+    def edit(self, spec, prefix):
+        # Only want to build delly source, not submodules. Build fails
+        # using provided submodules, succeeds with existing spack recipes.
+        makefile = FileFilter('Makefile')
+        makefile.filter('HTSLIBSOURCES =', '#HTSLIBSOURCES')
+        makefile.filter('BOOSTSOURCES =', '#BOOSTSOURCES')
+        makefile.filter('SEQTK_ROOT ?=', '#SEQTK_ROOT')
+        makefile.filter('BOOST_ROOT ?=', '#BOOST_ROOT')
+        makefile.filter('cd src', '# cd src')
+        makefile.filter('.htslib ', '')
+        makefile.filter('.bcftools ', '')
+        makefile.filter('.boost ', '')
+        makefile.filter('.htslib:', '# .htslib:')
+        makefile.filter('.bcftools:', '# .bcftools:')
+        makefile.filter('.boost:', '# .boost:')
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        with working_dir('src'):
+            install('delly', prefix.bin)
+            install('dpe', prefix.bin)
+            install('cov', prefix.bin)