py-mg-rast-tools: Create new package and its dependencies. (#7816)

* r-matr: Create new package.

* shocklibs: Create new package.

* r-biom-utils: Create new package.

* r-mgraster: Create new package

* py-poster: Create new package.

* py-requests-toolbelt: Create new package.

* perl-libwww-perl: Create new package.

* py-mg-rast-tools: Create new package.

* mg-rast-tools: Fix version constraints for dependencies.

* Change dependency type of py-setuptools.

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)