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authorDouglas Duckworth <quackmaster@protonmail.com>2017-05-12 15:11:20 -0400
committerAdam J. Stewart <ajstewart426@gmail.com>2017-05-12 14:11:20 -0500
commit360dc4a70962a8b7084b83a5194ec4e3b1ae5fa9 (patch)
treea2e8ee42b7725a4695053c9dedc3e2893072468d
parent4e13641db869b5660a2c2c56ec2130acd2fea8e7 (diff)
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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
-rw-r--r--var/spack/repos/builtin/packages/ont-albacore/package.py51
-rw-r--r--var/spack/repos/builtin/packages/py-cutadapt/package.py40
-rw-r--r--var/spack/repos/builtin/packages/py-ont-fast5-api/package.py43
-rw-r--r--var/spack/repos/builtin/packages/py-xopen/package.py40
4 files changed, 174 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))
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'))