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author | Douglas Duckworth <quackmaster@protonmail.com> | 2017-05-12 15:11:20 -0400 |
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committer | Adam J. Stewart <ajstewart426@gmail.com> | 2017-05-12 14:11:20 -0500 |
commit | 360dc4a70962a8b7084b83a5194ec4e3b1ae5fa9 (patch) | |
tree | a2e8ee42b7725a4695053c9dedc3e2893072468d /var/spack/repos/builtin/packages/ont-albacore | |
parent | 4e13641db869b5660a2c2c56ec2130acd2fea8e7 (diff) | |
download | spack-360dc4a70962a8b7084b83a5194ec4e3b1ae5fa9.tar.gz spack-360dc4a70962a8b7084b83a5194ec4e3b1ae5fa9.tar.bz2 spack-360dc4a70962a8b7084b83a5194ec4e3b1ae5fa9.tar.xz spack-360dc4a70962a8b7084b83a5194ec4e3b1ae5fa9.zip |
albacore and cutadapt again (#4219)
* 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
Diffstat (limited to 'var/spack/repos/builtin/packages/ont-albacore')
-rw-r--r-- | var/spack/repos/builtin/packages/ont-albacore/package.py | 51 |
1 files changed, 51 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/ont-albacore/package.py b/var/spack/repos/builtin/packages/ont-albacore/package.py new file mode 100644 index 0000000000..a9b6ea0661 --- /dev/null +++ b/var/spack/repos/builtin/packages/ont-albacore/package.py @@ -0,0 +1,51 @@ +############################################################################## +# 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)) |