phantompeakqualtools: new package (#6403)

2 files changed, 93 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/phantompeakqualtools/package.py b/var/spack/repos/builtin/packages/phantompeakqualtools/package.py
new file mode 100644
index 0000000000..6e82b9ec9e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/phantompeakqualtools/package.py
@@ -0,0 +1,44 @@
+##############################################################################
+# 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/spack/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 Phantompeakqualtools(RPackage):
+    """This package computes informative enrichment and quality measures for
+       ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data."""
+
+    homepage = "https://github.com/kundajelab/phantompeakqualtools"
+    url      = "https://github.com/kundajelab/phantompeakqualtools/archive/1.2.tar.gz"
+
+    version('1.2', 'e94943a42132b9ff2886f006ab34c121')
+
+    depends_on('awk')
+    depends_on('samtools')
+    depends_on('r', type=('build', 'run'))
+    depends_on('r-phantompeakqualtools', type=('build', 'run'))
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install('run_spp.R', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/r-phantompeakqualtools/package.py b/var/spack/repos/builtin/packages/r-phantompeakqualtools/package.py
new file mode 100644
index 0000000000..d32f402974
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-phantompeakqualtools/package.py
@@ -0,0 +1,49 @@
+##############################################################################
+# 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/spack/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 RPhantompeakqualtools(RPackage):
+    """Computes informative enrichment and quality measures for
+       ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. This is a modified version
+       of r-spp to be used in conjunction with the phantompeakqualtools
+       package."""
+
+    homepage = "https://github.com/kundajelab/phantompeakqualtools"
+    url      = "https://github.com/kundajelab/phantompeakqualtools/raw/master/spp_1.14.tar.gz"
+
+    version('1.14', '4de207d570999170c1bf45bcba8c6d2d')
+
+    depends_on('boost@1.41.0:')
+    depends_on('r-catools', type=('build', 'run'))
+    depends_on('r-snow', type=('build', 'run'))
+    depends_on('r-snowfall', type=('build', 'run'))
+    depends_on('r-bitops', type=('build', 'run'))
+    depends_on('r-rsamtools', type=('build', 'run'))
+
+    conflicts('%gcc@6:')
+
+    def setup_environment(self, spack_env, run_env):
+        spack_env.set('BOOST_ROOT', self.spec['boost'].prefix)