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

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'))