vegas2: new package (#5150)

* vegas2: new package

* small version things

4 files changed, 126 insertions, 1 deletions

diff --git a/var/spack/repos/builtin/packages/plink/package.py b/var/spack/repos/builtin/packages/plink/package.py
new file mode 100644
index 0000000000..a519f30184
--- /dev/null
+++ b/var/spack/repos/builtin/packages/plink/package.py
@@ -0,0 +1,41 @@
+##############################################################################
+# 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 Plink(Package):
+    """PLINK is a free, open-source whole genome association analysis toolset,
+       designed to perform a range of basic, large-scale analyses in a
+       computationally efficient manner."""
+
+    homepage = "https://www.cog-genomics.org/plink/1.9/"
+
+    version('1.9', 'a2325881594856c0f1b7523290d1e04f',
+            url='https://www.cog-genomics.org/static/bin/plink170815/plink_linux_x86_64.zip')
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install('plink', prefix.bin)
+        install('prettify', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/r-corpcor/package.py b/var/spack/repos/builtin/packages/r-corpcor/package.py
new file mode 100644
index 0000000000..09798cbd2d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-corpcor/package.py
@@ -0,0 +1,34 @@
+##############################################################################
+# 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 RCorpcor(RPackage):
+    """Efficient Estimation of Covariance and (Partial) Correlation"""
+
+    homepage = "https://cran.r-project.org/package=corpcor"
+    url      = "https://cran.r-project.org/src/contrib/corpcor_1.6.9.tar.gz"
+
+    version('1.6.9', '7f447d9f389e5d7dedb5fe5baedca925')
diff --git a/var/spack/repos/builtin/packages/r-mvtnorm/package.py b/var/spack/repos/builtin/packages/r-mvtnorm/package.py
index 31933e70a3..2df9206a63 100644
--- a/var/spack/repos/builtin/packages/r-mvtnorm/package.py
+++ b/var/spack/repos/builtin/packages/r-mvtnorm/package.py
@@ -30,6 +30,7 @@ class RMvtnorm(RPackage):
     deviates and densities."""
 
     homepage = "http://mvtnorm.r-forge.r-project.org/"
-    url      = "https://cran.r-project.org/src/contrib/mvtnorm_1.0-5.tar.gz"
+    url      = "https://cran.r-project.org/src/contrib/mvtnorm_1.0-6.tar.gz"
 
+    version('1.0-6', 'cb69426868fd3e330412b8491901d9d4')
     version('1.0-5', '5894dd3969bbfa26f4862c45f9a48a52')
diff --git a/var/spack/repos/builtin/packages/vegas2/package.py b/var/spack/repos/builtin/packages/vegas2/package.py
new file mode 100644
index 0000000000..1c091a568c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/vegas2/package.py
@@ -0,0 +1,49 @@
+##############################################################################
+# 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 Vegas2(Package):
+    """"VEGAS2 is an extension that uses 1,000 Genomes data to model SNP
+        correlations across the autosomes and chromosome X"""
+
+    homepage = "https://vegas2.qimrberghofer.edu.au/"
+    url      = "https://vegas2.qimrberghofer.edu.au/vegas2v2"
+
+    version('2', '815d80b86e9e294f99332bb5181e897a', expand=False)
+
+    depends_on('perl', type='run')
+    depends_on('r', type='run')
+    depends_on('plink')
+    depends_on('r-mvtnorm', type='run')
+    depends_on('r-corpcor', type='run')
+
+    def url_for_version(self, version):
+        url = 'https://vegas2.qimrberghofer.edu.au/vegas2v{0}'
+        return url.format(version)
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install('vegas2v{0}'.format(self.version), prefix.bin)