Feature/methycode (#5374)

* methylcode: added package

* pyfasta: added package

* py-bsddb3: added package

* py-bsddb3: added package

* Update package.py

* Update package.py

* Update package.py

* removed fixme comments

* Update package.py

* Update package.py

* Update package.py

* Update package.py

* Update package.py

* Update package.py

* Update package.py

* Update package.py

3 files changed, 123 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/py-bsddb3/package.py b/var/spack/repos/builtin/packages/py-bsddb3/package.py
new file mode 100644
index 0000000000..1ba1578238
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-bsddb3/package.py
@@ -0,0 +1,40 @@
+##############################################################################
+# Copyright (c) 2013-2017, 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 PyBsddb3(PythonPackage):
+    """This module provides a nearly complete wrapping of the Oracle/Sleepycat
+       C API for the Database Environment, Database, Cursor, Log Cursor,
+       Sequence and Transaction objects, and each of these is exposed
+       as a Python type in the bsddb3.db module."""
+
+    homepage = "://pypi.python.org/pypi/bsddb3/6.2.5"
+    url      = "https://pypi.python.org/packages/ba/a7/131dfd4e3a5002ef30e20bee679d5e6bcb2fcc6af21bd5079dc1707a132c/bsddb3-6.2.5.tar.gz#md5=610267c189964c905a931990e1ba438c"
+
+    version('6.2.5', '610267c189964c905a931990e1ba438c')
+
+    depends_on('python@2.6:')
+    depends_on('py-setuptools')
diff --git a/var/spack/repos/builtin/packages/py-methylcode/package.py b/var/spack/repos/builtin/packages/py-methylcode/package.py
new file mode 100644
index 0000000000..9bdeed71ca
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-methylcode/package.py
@@ -0,0 +1,44 @@
+##############################################################################
+# Copyright (c) 2013-2017, 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 PyMethylcode(PythonPackage):
+    """MethylCoder is a single program that takes of bisulfite-treated
+       reads and outputs per-base methylation data. """
+
+    homepage = "https://github.com/brentp/methylcode"
+    url      = "https://github.com/brentp/methylcode/archive/master.zip"
+
+    version('1.0.0', 'd0ba07c1ab2c74adddd1b23f8e5823e7')
+
+    depends_on('python@2.7.0:2.7.999')
+    depends_on('py-six')
+    depends_on('py-setuptools')
+    depends_on('py-numpy')
+    depends_on('py-pyparsing')
+    depends_on('py-pyfasta')
+    depends_on('py-bsddb3')
+    depends_on('bowtie')
diff --git a/var/spack/repos/builtin/packages/py-pyfasta/package.py b/var/spack/repos/builtin/packages/py-pyfasta/package.py
new file mode 100644
index 0000000000..b346afe551
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-pyfasta/package.py
@@ -0,0 +1,39 @@
+##############################################################################
+# Copyright (c) 2013-2017, 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 PyPyfasta(PythonPackage):
+    """Pyfasta: fast, memory-efficient, pythonic (and command-line)
+       access to fasta sequence files"""
+
+    homepage = "https://pypi.python.org/pypi/pyfasta/"
+    url      = "https://pypi.python.org/packages/be/3f/794fbcdaaa2113f0a1d16a962463896c1a6bdab77bd63f33a8f16aae6cdc/pyfasta-0.5.2.tar.gz"
+
+    version('0.5.2', 'bf61ab997dca329675c3eb2ee7cdfcf2')
+
+    depends_on('python@2.6:')
+    depends_on('py-setuptools')
+    depends_on('py-numpy')