py-deeptools: new package and dependencies (#4717)

* py-deeptools: new package and dependencies

* py-deeptools: fixing python things

* missed a fix

5 files changed, 159 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/bcftools/package.py b/var/spack/repos/builtin/packages/bcftools/package.py
index 6a276709ef..6555692fab 100644
--- a/var/spack/repos/builtin/packages/bcftools/package.py
+++ b/var/spack/repos/builtin/packages/bcftools/package.py
@@ -39,6 +39,8 @@ class Bcftools(Package):
 
     depends_on('zlib')
     depends_on('bzip2', when="@1.4:")
+    # build fails without xz
+    depends_on('xz', when="@1.4")
 
     def install(self, spec, prefix):
         make("prefix=%s" % prefix, "all")
diff --git a/var/spack/repos/builtin/packages/py-deeptools/package.py b/var/spack/repos/builtin/packages/py-deeptools/package.py
new file mode 100644
index 0000000000..e4e1ec2583
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-deeptools/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 PyDeeptools(PythonPackage):
+    """deepTools addresses the challenge of handling the large amounts of data
+       that are now routinely generated from DNA sequencing centers."""
+
+    homepage = "https://pypi.io/packages/source/d/deepTools"
+    url      = "https://pypi.io/packages/source/d/deepTools/deepTools-2.5.2.tar.gz"
+
+    version('2.5.2', 'ba8a44c128c6bb1ed4ebdb20bf9ae9c2')
+
+    depends_on('python@2.7:', type=('build', 'run'))
+    depends_on('py-setuptools', type='build')
+    depends_on('py-numpy@1.9.0:', type=('build', 'run'))
+    depends_on('py-scipy@0.17.0:', type=('build', 'run'))
+    depends_on('py-py2bit@0.2.0:', type=('build', 'run'))
+    depends_on('py-pybigwig@0.2.1:', type=('build', 'run'))
+    depends_on('py-pysam@0.8.2:', type=('build', 'run'))
+    depends_on('py-matplotlib@1.4.0:', type=('build', 'run'))
+    depends_on('py-numpydoc@0.5:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-py2bit/package.py b/var/spack/repos/builtin/packages/py-py2bit/package.py
new file mode 100644
index 0000000000..d48fb7e9b9
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-py2bit/package.py
@@ -0,0 +1,36 @@
+##############################################################################
+# 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 PyPy2bit(PythonPackage):
+    """A package for accessing 2bit files using lib2bit."""
+
+    homepage = "https://pypi.python.org/pypi/py2bit"
+    url      = "https://pypi.io/packages/source/p/py2bit/py2bit-0.2.1.tar.gz"
+
+    version('0.2.1', 'eaf5b1c80a0bbf0b35af1f002f83a556')
+
+    depends_on('py-setuptools', type='build')
diff --git a/var/spack/repos/builtin/packages/py-pybigwig/package.py b/var/spack/repos/builtin/packages/py-pybigwig/package.py
new file mode 100644
index 0000000000..4d96ba58c0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-pybigwig/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 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 PyPybigwig(PythonPackage):
+    """A package for accessing bigWig files using libBigWig."""
+
+    homepage = "https://pypi.python.org/pypi/pyBigWig"
+    url      = "https://pypi.io/packages/source/p/pyBigWig/pyBigWig-0.3.4.tar.gz"
+
+    version('0.3.4', '8e0a91e26e87eeaa071408a3a749bfa9')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('curl', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-pysam/package.py b/var/spack/repos/builtin/packages/py-pysam/package.py
new file mode 100644
index 0000000000..cf470ea564
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-pysam/package.py
@@ -0,0 +1,39 @@
+##############################################################################
+# 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 PyPysam(PythonPackage):
+    """A python module for reading, manipulating and writing genomic data
+       sets."""
+
+    homepage = "https://pypi.python.org/pypi/pysam"
+    url      = "https://pypi.io/packages/source/p/pysam/pysam-0.11.2.2.tar.gz"
+
+    version('0.11.2.2', '56230cd5f55b503845915b76c22d620a')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-cython@0.21:', type='build')
+    depends_on('bcftools')