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
This commit is contained in:
Audrey Thoma
Adam J. Stewart
parent
79f9548a9a
commit
1f578c5777
4 changed files with 217 additions and 0 deletions
44
var/spack/repos/builtin/packages/itsx/package.py
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44
var/spack/repos/builtin/packages/itsx/package.py
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##############################################################################
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# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
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# Produced at the Lawrence Livermore National Laboratory.
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#
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# This file is part of Spack.
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# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
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# LLNL-CODE-647188
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#
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# For details, see https://github.com/llnl/spack
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# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
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#
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# This program is free software; you can redistribute it and/or modify
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# it under the terms of the GNU Lesser General Public License (as
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# published by the Free Software Foundation) version 2.1, February 1999.
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#
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# This program is distributed in the hope that it will be useful, but
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# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
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# conditions of the GNU Lesser General Public License for more details.
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#
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# You should have received a copy of the GNU Lesser General Public
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# License along with this program; if not, write to the Free Software
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# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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##############################################################################
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from spack import *
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class Itsx(Package):
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"""Improved software detection and extraction of ITS1 and ITS2 from
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ribosomal ITS sequences of fungi and other eukaryotes for use in
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environmental sequencing"""
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homepage = "http://microbiology.se/software/itsx/"
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url = "http://microbiology.se/sw/ITSx_1.0.11.tar.gz"
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version('1.0.11', '1bff12f1d5742f19be6ca585e9bf81fa')
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depends_on('perl', type=('build', 'run'))
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depends_on('hmmer')
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def install(self, spec, prefix):
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mkdirp(prefix.bin)
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install('ITSx', prefix.bin)
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install_tree('ITSx_db', prefix.bin.ITSx_db)
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48
var/spack/repos/builtin/packages/py-biom-format/package.py
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var/spack/repos/builtin/packages/py-biom-format/package.py
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##############################################################################
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# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
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# Produced at the Lawrence Livermore National Laboratory.
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#
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# This file is part of Spack.
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# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
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# LLNL-CODE-647188
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#
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# For details, see https://github.com/llnl/spack
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# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
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#
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# This program is free software; you can redistribute it and/or modify
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# it under the terms of the GNU Lesser General Public License (as
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# published by the Free Software Foundation) version 2.1, February 1999.
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#
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# This program is distributed in the hope that it will be useful, but
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# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
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# conditions of the GNU Lesser General Public License for more details.
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#
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# You should have received a copy of the GNU Lesser General Public
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# License along with this program; if not, write to the Free Software
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# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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##############################################################################
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from spack import *
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class PyBiomFormat(PythonPackage):
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"""The BIOM file format (canonically pronounced biome) is designed to be
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a general-use format for representing biological sample by observation
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contingency tables."""
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homepage = "https://pypi.python.org/pypi/biom-format/2.1.6"
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url = "https://pypi.io/packages/source/b/biom-format/biom-format-2.1.6.tar.gz"
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version('2.1.6', '1dd4925b74c56e8ee864d5e1973068de')
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variant('h5py', default=True, description='For use with BIOM 2.0+ files')
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depends_on('py-setuptools', type='build')
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depends_on('py-cython', type='build')
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depends_on('py-h5py', type=('build', 'run'), when='+h5py')
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depends_on('py-click', type=('build', 'run'))
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depends_on('py-numpy@1.3.0:', type=('build', 'run'))
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depends_on('py-future@0.16.0:', type=('build', 'run'))
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depends_on('py-scipy@0.13.0:', type=('build', 'run'))
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depends_on('py-pandas@0.19.2:', type=('build', 'run'))
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depends_on('py-six@1.10.0:', type=('build', 'run'))
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80
var/spack/repos/builtin/packages/py-pipits/package.py
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var/spack/repos/builtin/packages/py-pipits/package.py
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##############################################################################
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# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
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# Produced at the Lawrence Livermore National Laboratory.
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#
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# This file is part of Spack.
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# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
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# LLNL-CODE-647188
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#
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# For details, see https://github.com/llnl/spack
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# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
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#
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# This program is free software; you can redistribute it and/or modify
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# it under the terms of the GNU Lesser General Public License (as
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# published by the Free Software Foundation) version 2.1, February 1999.
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#
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# This program is distributed in the hope that it will be useful, but
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# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
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# conditions of the GNU Lesser General Public License for more details.
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#
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# You should have received a copy of the GNU Lesser General Public
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# License along with this program; if not, write to the Free Software
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# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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##############################################################################
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from spack import *
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class PyPipits(PythonPackage):
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"""Automated pipeline for analyses of fungal ITS from the Illumina"""
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homepage = "https://github.com/hsgweon/pipits"
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url = "https://github.com/hsgweon/pipits/archive/1.5.0.tar.gz"
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version('1.5.0', '3f9b52bd7ffbcdb96d7bec150275070a')
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depends_on('python@:2.999', type=('build', 'run'))
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depends_on('py-biom-format', type=('build', 'run'))
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depends_on('py-numpy', type=('build', 'run'))
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depends_on('java', type=('build', 'run'))
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depends_on('hmmer')
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depends_on('fastx-toolkit')
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depends_on('vsearch')
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depends_on('itsx')
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depends_on('rdp-classifier')
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resource(
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name='UNITE_retrained',
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url='http://sourceforge.net/projects/pipits/files/UNITE_retrained_28.06.2017.tar.gz',
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destination='refdb'
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)
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resource(
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name='uchime_reference_dataset_01.01.2016.fasta',
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url='https://unite.ut.ee/sh_files/uchime_reference_dataset_01.01.2016.zip',
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destination=join_path('refdb', 'uchime_reference_dataset_01.01.2016')
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)
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resource(
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name='warcup_retrained_V2',
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url='https://sourceforge.net/projects/pipits/files/warcup_retrained_V2.tar.gz',
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destination='refdb'
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)
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@run_after('install')
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def install_db(self):
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install_tree(join_path(self.stage.source_path, 'refdb'),
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self.prefix.refdb)
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def setup_environment(self, spack_env, run_env):
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run_env.set('PIPITS_UNITE_REFERENCE_DATA_CHIMERA', join_path(
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self.prefix, 'refdb',
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'uchime_reference_dataset_01.01.2016',
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'uchime_reference_dataset_01.01.2016.fasta'))
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run_env.set('PIPITS_UNITE_RETRAINED_DIR',
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self.prefix.refdb.UNITE_retrained)
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run_env.set('PIPITS_WARCUP_RETRAINED_DIR',
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self.prefix.refdb.warcup_retrained_V2)
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run_env.set('PIPITS_RDP_CLASSIFIER_JAR', join_path(
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self.spec['rdp-classifier'].prefix.bin,
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'classifier.jar'))
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45
var/spack/repos/builtin/packages/rdp-classifier/package.py
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var/spack/repos/builtin/packages/rdp-classifier/package.py
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@ -0,0 +1,45 @@
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##############################################################################
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# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
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# Produced at the Lawrence Livermore National Laboratory.
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#
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# This file is part of Spack.
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# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
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# LLNL-CODE-647188
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#
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# For details, see https://github.com/llnl/spack
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# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
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#
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# This program is free software; you can redistribute it and/or modify
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# it under the terms of the GNU Lesser General Public License (as
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# published by the Free Software Foundation) version 2.1, February 1999.
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#
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# This program is distributed in the hope that it will be useful, but
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# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
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# conditions of the GNU Lesser General Public License for more details.
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#
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# You should have received a copy of the GNU Lesser General Public
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# License along with this program; if not, write to the Free Software
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# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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##############################################################################
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from spack import *
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class RdpClassifier(Package):
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"""The RDP Classifier is a naive Bayesian classifier that can rapidly and
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accurately provides taxonomic assignments from domain to genus, with
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confidence estimates for each assignment. """
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homepage = "http://rdp.cme.msu.edu/"
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url = "https://downloads.sourceforge.net/project/rdp-classifier/rdp-classifier/rdp_classifier_2.12.zip"
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version('2.12', '7fdfa33512629810f0ff06b905642ddd')
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depends_on('java', type=('build', 'run'))
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def install(self, spec, prefix):
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mkdirp(prefix.bin)
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install(join_path('dist', 'classifier.jar'), prefix.bin)
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install_tree(join_path('dist', 'lib'), prefix.bin.lib)
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install(join_path('lib', 'junit-4.8.2.jar'), prefix.bin.lib)
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install_tree('src', prefix.src)
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