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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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var/spack/repos/builtin/packages/ont-albacore/package.py Normal file
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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))