cleaveland4: new package (#4894)

* cleaveland4: new package

* fixing return line in viennarna url_for_version

3 files changed, 150 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/cleaveland4/package.py b/var/spack/repos/builtin/packages/cleaveland4/package.py
new file mode 100644
index 0000000000..505f800ac7
--- /dev/null
+++ b/var/spack/repos/builtin/packages/cleaveland4/package.py
@@ -0,0 +1,48 @@
+##############################################################################
+# Copyright (c) 2013-2016, 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 Cleaveland4(Package):
+    """CleaveLand4: Analysis of degradome data to find sliced miRNA and siRNA
+       targets"""
+
+    homepage = "https://github.com/MikeAxtell/CleaveLand4"
+    url      = "https://github.com/MikeAxtell/CleaveLand4/archive/v4.4.tar.gz"
+
+    version('4.4', 'cf62a1de715a612fc8bd5a62364e69db')
+
+    depends_on('perl', type=('build', 'run'))
+    depends_on('perl-math-cdf', type=('build', 'run'))
+    depends_on('bowtie')
+    depends_on('viennarna')
+    depends_on('r', type=('build', 'run'))
+    depends_on('samtools')
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install('CleaveLand4.pl', prefix.bin)
+        with working_dir('GSTAr_v1-0'):
+            install('GSTAr.pl', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/perl-math-cdf/package.py b/var/spack/repos/builtin/packages/perl-math-cdf/package.py
new file mode 100644
index 0000000000..6d7d195dea
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-math-cdf/package.py
@@ -0,0 +1,35 @@
+##############################################################################
+# Copyright (c) 2013-2016, 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 PerlMathCdf(PerlPackage):
+    """Generate probabilities and quantiles from several statistical
+       probability functions"""
+
+    homepage = "http://search.cpan.org/~callahan/Math-CDF-0.1/CDF.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/C/CA/CALLAHAN/Math-CDF-0.1.tar.gz"
+
+    version('0.1', '7866c7b6b9d27f0ce4b7637334478ab7')
diff --git a/var/spack/repos/builtin/packages/viennarna/package.py b/var/spack/repos/builtin/packages/viennarna/package.py
new file mode 100644
index 0000000000..548aacb56f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/viennarna/package.py
@@ -0,0 +1,67 @@
+##############################################################################
+# Copyright (c) 2013-2016, 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 Viennarna(AutotoolsPackage):
+    """The ViennaRNA Package consists of a C code library and several
+       stand-alone programs for the prediction and comparison of RNA secondary
+       structures."""
+
+    homepage = "https://www.tbi.univie.ac.at/RNA/"
+    url      = "https://www.tbi.univie.ac.at/RNA/download/sourcecode/2_3_x/ViennaRNA-2.3.5.tar.gz"
+
+    version('2.3.5', '4542120adae9b7abb605e2304c2a1326')
+
+    variant('sse', default=True, description='Enable SSE in order to substantially speed up execution')
+    variant('perl', default=True, description='Build ViennaRNA with Perl interface')
+    variant('python', default=True, description='Build ViennaRNA with Python interface')
+
+    depends_on('perl', type=('build', 'run'))
+    depends_on('python', type=('build', 'run'))
+    depends_on('libsvm')
+    depends_on('gsl')
+
+    def url_for_version(self, version):
+        url = 'https://www.tbi.univie.ac.at/RNA/download/sourcecode/{0}_x/ViennaRNA-{1}.tar.gz'
+        return url.format(version.up_to(2).underscored, version)
+
+    def configure_args(self):
+        args = []
+        if '+sse' in self.spec:
+            args.append('--enable-sse')
+        else:
+            args.append('--disable-sse')
+        if '~python' in self.spec:
+            args.append('--without-python')
+        else:
+            args.append('--with-python')
+        if '~perl' in self.spec:
+            args.append('--without-perl')
+        else:
+            args.append('--with-perl')
+        if 'python@3:' in self.spec:
+            args.append('--with-python3')
+        return args