From 1f578c57778bbab74c3c83cc700cf0d313433692 Mon Sep 17 00:00:00 2001 From: Audrey Thoma Date: Wed, 9 Aug 2017 15:04:21 -0500 Subject: [PATCH] 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 --- .../repos/builtin/packages/itsx/package.py | 44 ++++++++++ .../packages/py-biom-format/package.py | 48 +++++++++++ .../builtin/packages/py-pipits/package.py | 80 +++++++++++++++++++ .../packages/rdp-classifier/package.py | 45 +++++++++++ 4 files changed, 217 insertions(+) create mode 100644 var/spack/repos/builtin/packages/itsx/package.py create mode 100644 var/spack/repos/builtin/packages/py-biom-format/package.py create mode 100644 var/spack/repos/builtin/packages/py-pipits/package.py create mode 100644 var/spack/repos/builtin/packages/rdp-classifier/package.py 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)