diff options
8 files changed, 316 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/perl-libwww-perl/package.py b/var/spack/repos/builtin/packages/perl-libwww-perl/package.py new file mode 100644 index 0000000000..bf6a277bb6 --- /dev/null +++ b/var/spack/repos/builtin/packages/perl-libwww-perl/package.py @@ -0,0 +1,37 @@ +############################################################################## +# Copyright (c) 2013-2018, 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/spack/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 PerlLibwwwPerl(PerlPackage): + """The libwww-perl collection is a set of Perl modules which provides + a simple and consistent application programming interface to the + World-Wide Web. The main focus of the library is to provide classes and + functions that allow you to write WWW clients.""" + + homepage = "https://github.com/libwww-perl/libwww-perl" + url = "http://search.cpan.org/CPAN/authors/id/O/OA/OALDERS/libwww-perl-6.33.tar.gz" + + version('6.33', '2e15c1c789ac9036c99d094e47e3da23') diff --git a/var/spack/repos/builtin/packages/py-mg-rast-tools/package.py b/var/spack/repos/builtin/packages/py-mg-rast-tools/package.py new file mode 100644 index 0000000000..4b23651842 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-mg-rast-tools/package.py @@ -0,0 +1,50 @@ +############################################################################## +# Copyright (c) 2013-2018, 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/spack/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 PyMgRastTools(PythonPackage): + """Repository of scripts and libraries for using the MG-RAST API and + MG-RAST data.""" + + homepage = "https://github.com/MG-RAST/MG-RAST-Tools" + + version('2018.04.17', git='https://github.com/MG-RAST/MG-RAST-Tools.git', commit='a40c6e6539ad0bc1c08e1b03dfc0a9759755a326') + + depends_on('perl', type=('build', 'run')) + depends_on('py-setuptools@28.0:', type='build') + depends_on('py-prettytable@0.7:', type=('build', 'run')) + depends_on('py-poster@0.8.1:', type=('build', 'run')) + depends_on('py-requests', type=('build', 'run')) + depends_on('py-requests-toolbelt@0.8:', type=('build', 'run')) + depends_on('py-scipy', type=('build', 'run')) + depends_on('py-numpy', type=('build', 'run')) + depends_on('r-matr', type=('build', 'run')) + depends_on('shocklibs@0.1.30:') + depends_on('perl-list-moreutils', type=('build', 'run')) + depends_on('perl-exporter-tiny', type=('build', 'run')) + depends_on('perl-libwww-perl', type=('build', 'run')) + depends_on('perl-http-message', type=('build', 'run')) + depends_on('perl-json', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-poster/package.py b/var/spack/repos/builtin/packages/py-poster/package.py new file mode 100644 index 0000000000..100f11fe33 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-poster/package.py @@ -0,0 +1,36 @@ +############################################################################## +# Copyright (c) 2013-2018, 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/spack/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 PyPoster(PythonPackage): + """Streaming HTTP uploads and multipart/form-data encoding.""" + + homepage = "https://pypi.org/project/poster/" + url = "https://atlee.ca/software/poster/dist/0.8.1/poster-0.8.1.tar.gz" + + version('0.8.1', '2db12704538781fbaa7e63f1505d6fc8') + + depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-requests-toolbelt/package.py b/var/spack/repos/builtin/packages/py-requests-toolbelt/package.py new file mode 100644 index 0000000000..8d46e8d544 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-requests-toolbelt/package.py @@ -0,0 +1,38 @@ +############################################################################## +# Copyright (c) 2013-2018, 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/spack/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 PyRequestsToolbelt(PythonPackage): + """A toolbelt of useful classes and functions to be used with + python-requests""" + + homepage = "https://toolbelt.readthedocs.org/" + url = "https://github.com/requests/toolbelt/archive/0.8.0.tar.gz" + + version('0.8.0', 'de9bf7fbcc6ae341a5c4fd9f8912bcac') + + depends_on('py-setuptools', type='build') + depends_on('py-requests@2.0.1:3.0.0', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-biom-utils/package.py b/var/spack/repos/builtin/packages/r-biom-utils/package.py new file mode 100644 index 0000000000..fb27071d49 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-biom-utils/package.py @@ -0,0 +1,38 @@ +############################################################################## +# Copyright (c) 2013-2018, 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/spack/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 RBiomUtils(RPackage): + """Provides utilities to facilitate import, export and computation with + the BIOM (Biological Observation Matrix) format (http://biom-format.org). + """ + + homepage = "https://github.com/braithwaite/BIOM.utils/" + url = "https://cran.r-project.org/src/contrib/BIOM.utils_0.9.tar.gz" + + version('0.9', '980f08fd9848242007753cd27a998060') + + depends_on('r@3:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-matr/package.py b/var/spack/repos/builtin/packages/r-matr/package.py new file mode 100644 index 0000000000..b7a146c324 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-matr/package.py @@ -0,0 +1,42 @@ +############################################################################## +# Copyright (c) 2013-2018, 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/spack/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 RMatr(RPackage): + """Package matR (Metagenomics Analysis Tools for R) is an analysis + client for the MG-RAST metagenome annotation engine, part of the US + Department of Energy (DOE) Systems Biology Knowledge Base (KBase). + Customized analysis and visualization tools securely access remote + data and metadata within the popular open source R language and + environment for statistical computing.""" + + homepage = "https://github.com/MG-RAST/matR" + url = "https://cran.r-project.org/src/contrib/Archive/matR/matR_0.9.tar.gz" + + version('0.9', 'e2be8734009f5c5b9c1f6b677a77220a') + + depends_on('r-mgraster', type=('build', 'run')) + depends_on('r-biom-utils', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-mgraster/package.py b/var/spack/repos/builtin/packages/r-mgraster/package.py new file mode 100644 index 0000000000..bca66dc250 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-mgraster/package.py @@ -0,0 +1,38 @@ +############################################################################## +# Copyright (c) 2013-2018, 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/spack/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 RMgraster(RPackage): + """Convenience Functions for R Language Access to the v.1 API of the + MG-RAST Metagenome Annotation Server, part of the US Department of Energy + (DOE) Systems Biology Knowledge Base (KBase).""" + + homepage = "https://github.com/braithwaite/MGRASTer/" + url = "https://cran.r-project.org/src/contrib/MGRASTer_0.9.tar.gz" + + version('0.9', '902c7ad4180b858d6b6428ea26d7652a') + + depends_on('r@3:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/shocklibs/package.py b/var/spack/repos/builtin/packages/shocklibs/package.py new file mode 100644 index 0000000000..7f399de02c --- /dev/null +++ b/var/spack/repos/builtin/packages/shocklibs/package.py @@ -0,0 +1,37 @@ +############################################################################## +# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of99c6c1b375f7f3 Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/spack/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 Shocklibs(Package): + """The lib for shock: An object store for scientific data.""" + + homepage = "https://github.com/MG-RAST/Shock" + url = "https://github.com/MG-RAST/Shock/archive/v0.9.24.tar.gz" + + version('0.9.24', '98b2e91e2726c7165f75afaf0ca51a5b') + + def install(self, spec, prefix): + install_tree('libs', prefix.libs) |