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albacore and cutadapt again (#4219)

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* added albacore package as well as dependency py-ont-fast5-api

* added py-cutadapt and dependency py-xopen

* made more changes to albacore and cutadapt as well as dependencies

* made changes again per @adamjstewart

* fixed by python n00b errors i think

* fixed?

* tw=79

* made changes to py-ont-fast5-api ont-albacore

* removed bad characters
This commit is contained in:
Douglas Duckworth 2017-05-12 15:11:20 -04:00 committed by Adam J. Stewart
parent 4e13641db8
commit 360dc4a709
4 changed files with 174 additions and 0 deletions
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##############################################################################
# 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 OntAlbacore(Package):
"""Albacore is a software project that provides an entry point to the Oxford
Nanopore basecalling algorithms. It can be run from the command line on
Windows and multiple Linux platforms. A selection of configuration files
allow basecalling DNA libraries made with our current range of sequencing
kits and Flow Cells."""
homepage = "https://nanoporetech.com"
url = "https://mirror.oxfordnanoportal.com/software/analysis/ont_albacore-1.1.0-cp35-cp35m-manylinux1_x86_64.whl"
version('1.1.0', 'fab4502ea1bad99d813aa2629e03e83d', expand=False)
extends('python')
depends_on('python@3.5.0:3.5.999', type=('build', 'run'))
depends_on('py-setuptools', type=('build'))
depends_on('py-numpy', type=('build', 'run'))
depends_on('py-dateutil', type=('build', 'run'))
depends_on('py-h5py', type=('build', 'run'))
depends_on('py-ont-fast5-api', type=('build', 'run'))
depends_on('py-pip', type=('build'))
def install(self, spec, prefix):
pip = which('pip')
pip('install', self.stage.archive_file, '--prefix={0}'.format(prefix))

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##############################################################################
# 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 PyCutadapt(PythonPackage):
"""Cutadapt finds and removes adapter sequences, primers, poly-A tails and
other types of unwanted sequence from your high-throughput sequencing
reads."""
homepage = "https://cutadapt.readthedocs.io"
url = "https://pypi.io/packages/source/c/cutadapt/cutadapt-1.13.tar.gz"
version('1.13', '2d2d14e0c20ad53d7d84b57bc3e63b4c')
depends_on('python@2.6:', type=('build', 'run'))
depends_on('py-setuptools', type=('build'))
depends_on('py-xopen@0.1.1:', type=('build', 'run'))

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##############################################################################
# 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 PyOntFast5Api(PythonPackage):
"""This project provides classes and utility functions for working with
read fast5 files. It provides an abstraction layer between the underlying
h5py library and the various concepts central to read fast5 files, such as
"reads", "analyses", "analysis summaries", and "analysis datasets".
Ideally all interaction with a read fast5 file should be possible via this
API, without having to directly invoke the h5py library."""
homepage = "https://github.com/nanoporetech/ont_fast5_api"
url = "https://pypi.io/packages/source/o/ont-fast5-api/ont-fast5-api-0.3.2.tar.gz"
version('0.3.2', '2ccfdbcd55239ffae712bb6e70ebfe8c')
depends_on('py-setuptools', type='build')
depends_on('py-h5py', type=('build', 'run'))
depends_on('py-numpy@1.8.1:', type=('build', 'run'))

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##############################################################################
# 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 PyXopen(PythonPackage):
"""This small Python module provides a xopen function that works like the
built-in open function, but can also deal with compressed files. Supported
compression formats are gzip, bzip2 and xz. They are automatically
recognized by their file extensions .gz, .bz2 or .xz."""
homepage = "https://github.com/marcelm/xopen"
url = "https://pypi.io/packages/source/x/xopen/xopen-0.1.1.tar.gz"
version('0.1.1', '4e0e955546ee6bee4ea736b54623a671')
depends_on('py-setuptools', type='build')
depends_on('python@2.6:', type=('build', 'run'))