pipits: new package (#5041)

* pipits: new package and dependencies

* fixing rdp-classifier java dep

* adding resources to pipits and fixing deps for py-biom-format

4 files changed, 217 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/itsx/package.py b/var/spack/repos/builtin/packages/itsx/package.py
new file mode 100644
index 0000000000..41b0d9a6a2
--- /dev/null
+++ b/var/spack/repos/builtin/packages/itsx/package.py
@@ -0,0 +1,44 @@
+##############################################################################
+# 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 Itsx(Package):
+    """Improved software detection and extraction of ITS1 and ITS2 from
+       ribosomal ITS sequences of fungi and other eukaryotes for use in
+       environmental sequencing"""
+
+    homepage = "http://microbiology.se/software/itsx/"
+    url      = "http://microbiology.se/sw/ITSx_1.0.11.tar.gz"
+
+    version('1.0.11', '1bff12f1d5742f19be6ca585e9bf81fa')
+
+    depends_on('perl', type=('build', 'run'))
+    depends_on('hmmer')
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install('ITSx', prefix.bin)
+        install_tree('ITSx_db', prefix.bin.ITSx_db)
diff --git a/var/spack/repos/builtin/packages/py-biom-format/package.py b/var/spack/repos/builtin/packages/py-biom-format/package.py
new file mode 100644
index 0000000000..2d61507bd0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-biom-format/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 PyBiomFormat(PythonPackage):
+    """The BIOM file format (canonically pronounced biome) is designed to be
+       a general-use format for representing biological sample by observation
+       contingency tables."""
+
+    homepage = "https://pypi.python.org/pypi/biom-format/2.1.6"
+    url      = "https://pypi.io/packages/source/b/biom-format/biom-format-2.1.6.tar.gz"
+
+    version('2.1.6', '1dd4925b74c56e8ee864d5e1973068de')
+
+    variant('h5py', default=True, description='For use with BIOM 2.0+ files')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-cython', type='build')
+    depends_on('py-h5py', type=('build', 'run'), when='+h5py')
+    depends_on('py-click', type=('build', 'run'))
+    depends_on('py-numpy@1.3.0:', type=('build', 'run'))
+    depends_on('py-future@0.16.0:', type=('build', 'run'))
+    depends_on('py-scipy@0.13.0:', type=('build', 'run'))
+    depends_on('py-pandas@0.19.2:', type=('build', 'run'))
+    depends_on('py-six@1.10.0:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-pipits/package.py b/var/spack/repos/builtin/packages/py-pipits/package.py
new file mode 100644
index 0000000000..88a629cc2e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-pipits/package.py
@@ -0,0 +1,80 @@
+##############################################################################
+# 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 PyPipits(PythonPackage):
+    """Automated pipeline for analyses of fungal ITS from the Illumina"""
+
+    homepage = "https://github.com/hsgweon/pipits"
+    url      = "https://github.com/hsgweon/pipits/archive/1.5.0.tar.gz"
+
+    version('1.5.0', '3f9b52bd7ffbcdb96d7bec150275070a')
+
+    depends_on('python@:2.999', type=('build', 'run'))
+    depends_on('py-biom-format', type=('build', 'run'))
+    depends_on('py-numpy', type=('build', 'run'))
+    depends_on('java', type=('build', 'run'))
+    depends_on('hmmer')
+    depends_on('fastx-toolkit')
+    depends_on('vsearch')
+    depends_on('itsx')
+    depends_on('rdp-classifier')
+
+    resource(
+        name='UNITE_retrained',
+        url='http://sourceforge.net/projects/pipits/files/UNITE_retrained_28.06.2017.tar.gz',
+        destination='refdb'
+    )
+
+    resource(
+        name='uchime_reference_dataset_01.01.2016.fasta',
+        url='https://unite.ut.ee/sh_files/uchime_reference_dataset_01.01.2016.zip',
+        destination=join_path('refdb', 'uchime_reference_dataset_01.01.2016')
+    )
+
+    resource(
+        name='warcup_retrained_V2',
+        url='https://sourceforge.net/projects/pipits/files/warcup_retrained_V2.tar.gz',
+        destination='refdb'
+    )
+
+    @run_after('install')
+    def install_db(self):
+        install_tree(join_path(self.stage.source_path, 'refdb'),
+                     self.prefix.refdb)
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.set('PIPITS_UNITE_REFERENCE_DATA_CHIMERA', join_path(
+                    self.prefix, 'refdb',
+                    'uchime_reference_dataset_01.01.2016',
+                    'uchime_reference_dataset_01.01.2016.fasta'))
+        run_env.set('PIPITS_UNITE_RETRAINED_DIR',
+                    self.prefix.refdb.UNITE_retrained)
+        run_env.set('PIPITS_WARCUP_RETRAINED_DIR',
+                    self.prefix.refdb.warcup_retrained_V2)
+        run_env.set('PIPITS_RDP_CLASSIFIER_JAR', join_path(
+                    self.spec['rdp-classifier'].prefix.bin,
+                    'classifier.jar'))
diff --git a/var/spack/repos/builtin/packages/rdp-classifier/package.py b/var/spack/repos/builtin/packages/rdp-classifier/package.py
new file mode 100644
index 0000000000..49cc367c8d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/rdp-classifier/package.py
@@ -0,0 +1,45 @@
+##############################################################################
+# 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 RdpClassifier(Package):
+    """The RDP Classifier is a naive Bayesian classifier that can rapidly and
+       accurately provides taxonomic assignments from domain to genus, with
+       confidence estimates for each assignment. """
+
+    homepage = "http://rdp.cme.msu.edu/"
+    url      = "https://downloads.sourceforge.net/project/rdp-classifier/rdp-classifier/rdp_classifier_2.12.zip"
+
+    version('2.12', '7fdfa33512629810f0ff06b905642ddd')
+
+    depends_on('java', type=('build', 'run'))
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install(join_path('dist', 'classifier.jar'), prefix.bin)
+        install_tree(join_path('dist', 'lib'), prefix.bin.lib)
+        install(join_path('lib', 'junit-4.8.2.jar'), prefix.bin.lib)
+        install_tree('src', prefix.src)