From 360dc4a70962a8b7084b83a5194ec4e3b1ae5fa9 Mon Sep 17 00:00:00 2001 From: Douglas Duckworth Date: Fri, 12 May 2017 15:11:20 -0400 Subject: 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 --- .../repos/builtin/packages/ont-albacore/package.py | 51 ++++++++++++++++++++++ .../repos/builtin/packages/py-cutadapt/package.py | 40 +++++++++++++++++ .../builtin/packages/py-ont-fast5-api/package.py | 43 ++++++++++++++++++ .../repos/builtin/packages/py-xopen/package.py | 40 +++++++++++++++++ 4 files changed, 174 insertions(+) create mode 100644 var/spack/repos/builtin/packages/ont-albacore/package.py create mode 100644 var/spack/repos/builtin/packages/py-cutadapt/package.py create mode 100644 var/spack/repos/builtin/packages/py-ont-fast5-api/package.py create mode 100644 var/spack/repos/builtin/packages/py-xopen/package.py (limited to 'var') 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)) diff --git a/var/spack/repos/builtin/packages/py-cutadapt/package.py b/var/spack/repos/builtin/packages/py-cutadapt/package.py new file mode 100644 index 0000000000..30c6c4332f --- /dev/null +++ b/var/spack/repos/builtin/packages/py-cutadapt/package.py @@ -0,0 +1,40 @@ +############################################################################## +# 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')) diff --git a/var/spack/repos/builtin/packages/py-ont-fast5-api/package.py b/var/spack/repos/builtin/packages/py-ont-fast5-api/package.py new file mode 100644 index 0000000000..d6aea1f5ec --- /dev/null +++ b/var/spack/repos/builtin/packages/py-ont-fast5-api/package.py @@ -0,0 +1,43 @@ +############################################################################## +# 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')) diff --git a/var/spack/repos/builtin/packages/py-xopen/package.py b/var/spack/repos/builtin/packages/py-xopen/package.py new file mode 100644 index 0000000000..0137bc476f --- /dev/null +++ b/var/spack/repos/builtin/packages/py-xopen/package.py @@ -0,0 +1,40 @@ +############################################################################## +# 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')) -- cgit v1.2.3-60-g2f50