From 5bb3538541b096149d7a9b123dd06ca0673239d3 Mon Sep 17 00:00:00 2001 From: ynanyam <31993194+ynanyam@users.noreply.github.com> Date: Sat, 16 Sep 2017 14:58:04 -0500 Subject: 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 --- .../repos/builtin/packages/py-bsddb3/package.py | 40 ++++++++++++++++++++ .../builtin/packages/py-methylcode/package.py | 44 ++++++++++++++++++++++ .../repos/builtin/packages/py-pyfasta/package.py | 39 +++++++++++++++++++ 3 files changed, 123 insertions(+) create mode 100644 var/spack/repos/builtin/packages/py-bsddb3/package.py create mode 100644 var/spack/repos/builtin/packages/py-methylcode/package.py create mode 100644 var/spack/repos/builtin/packages/py-pyfasta/package.py 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') -- cgit v1.2.3-70-g09d2