added py-multiqc and dependencies (#4381)

* added py-multiqc and dependencies

* added requested changes per #4381

* added colormath dependency per https://github.com/jsvine/spectra/blob/master/requirements.txt

* py-multiqc changes

* py-multiqc does not need colormath - spectra does

4 files changed, 160 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/py-colormath/package.py b/var/spack/repos/builtin/packages/py-colormath/package.py
new file mode 100644
index 0000000000..578673a709
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-colormath/package.py
@@ -0,0 +1,38 @@
+##############################################################################
+# 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 LICENSE file 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 PyColormath(PythonPackage):
+    """Color math and conversion library."""
+
+    homepage = "https://pypi.python.org/pypi/colormath/2.1.1"
+    url      = "https://pypi.io/packages/source/c/colormath/colormath-2.1.1.tar.gz"
+
+    version('2.1.1', '10a0fb17e3c24363d0e1a3f2dccaa33b')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-numpy', type=('build', 'run'))
+    depends_on('py-networkx', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-lzstring/package.py b/var/spack/repos/builtin/packages/py-lzstring/package.py
new file mode 100644
index 0000000000..75f0f606df
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-lzstring/package.py
@@ -0,0 +1,37 @@
+##############################################################################
+# 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 LICENSE file 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 PyLzstring(PythonPackage):
+    """lz-string for python."""
+
+    homepage = "https://github.com/gkovacs/lz-string-python"
+    url      = "https://pypi.io/packages/source/l/lzstring/lzstring-1.0.3.tar.gz"
+
+    version('1.0.3', '1c636543484629020a26432740f81443')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-future', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-multiqc/package.py b/var/spack/repos/builtin/packages/py-multiqc/package.py
new file mode 100644
index 0000000000..c0eb702974
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-multiqc/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 LICENSE file 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 PyMultiqc(PythonPackage):
+    """MultiQC is a tool to aggregate bioinformatics results across many
+    samples into a single report. It is written in Python and contains modules
+    for a large number of common bioinformatics tools."""
+
+    homepage = "https://multiqc.info"
+    url      = "https://pypi.io/packages/source/m/multiqc/multiqc-1.0.tar.gz"
+
+    version('1.0', '0b7310b3f75595e5be8099fbed2d2515')
+
+    depends_on('python@2.7:')
+    depends_on('py-setuptools', type='build')
+    depends_on('py-click', type=('build', 'run'))
+    depends_on('py-jinja2@2.9:', type=('build', 'run'))
+    depends_on('py-lzstring', type=('build', 'run'))
+    depends_on('py-future@0.14.1:', type=('build', 'run'))
+    depends_on('py-spectra', type=('build', 'run'))
+    depends_on('py-matplotlib', type=('build', 'run'))
+    depends_on('py-numpy', type=('build', 'run'))
+    depends_on('py-pyyaml', type=('build', 'run'))
+    depends_on('py-simplejson', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-spectra/package.py b/var/spack/repos/builtin/packages/py-spectra/package.py
new file mode 100644
index 0000000000..acb2643698
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-spectra/package.py
@@ -0,0 +1,37 @@
+##############################################################################
+# 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 LICENSE file 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 PySpectra(PythonPackage):
+    """Color scales and color conversion made easy for Python."""
+
+    homepage = "https://pypi.python.org/pypi/spectra/0.0.8"
+    url      = "https://pypi.io/packages/source/s/spectra/spectra-0.0.8.tar.gz"
+
+    version('0.0.8', '83020b29e584389f24c7720f38f0136c')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-colormath', type=('build', 'run'))