rtax: new package (#5025)

* rtax: new package

* fixing usearch version flexibility

2 files changed, 92 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/rtax/package.py b/var/spack/repos/builtin/packages/rtax/package.py
new file mode 100644
index 0000000000..c2b917a81e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/rtax/package.py
@@ -0,0 +1,43 @@
+##############################################################################
+# 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 Rtax(Package):
+    """Rapid and accurate taxonomic classification of short paired-end
+       sequence reads from the 16S ribosomal RNA gene"""
+
+    homepage = "https://github.com/davidsoergel/rtax"
+    url      = "http://static.davidsoergel.com/rtax-0.984.tgz"
+
+    version('0.984', 'e9dbbe4b3c26b0f0f6c14a5fb46aa587')
+
+    depends_on('usearch')
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install('rtax', prefix.bin)
+        install_tree('scripts', prefix.bin.scripts)
+        install_tree('greengenes', prefix.bin.greengenes)
diff --git a/var/spack/repos/builtin/packages/usearch/package.py b/var/spack/repos/builtin/packages/usearch/package.py
new file mode 100644
index 0000000000..87ea6798ca
--- /dev/null
+++ b/var/spack/repos/builtin/packages/usearch/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 *
+import os
+
+
+class Usearch(Package):
+    """USEARCH is a unique sequence analysis tool with thousands of users
+       world-wide.
+
+       Note: A manual download is required for USEARCH.
+       Spack will search your current directory for the download file.
+       Alternatively, add this file to a mirror so that Spack can find it.
+       For instructions on how to set up a mirror, see
+       http://spack.readthedocs.io/en/latest/mirrors.html"""
+
+    homepage = "http://www.drive5.com/usearch/"
+
+    version('10.0.240', '05192b6d5e291530c190a19a3cc82b53', expand=False)
+
+    def url_for_version(self, version):
+        return "file://{0}/usearch{1}_i86linux32".format(os.getcwd(), version)
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install('usearch{0}_i86linux32'.format(self.version),
+                prefix.bin.usearch)