From 3eedbd7c4ecac9573a799947ffd679cd04cc1051 Mon Sep 17 00:00:00 2001 From: Audrey Thoma Date: Thu, 13 Jul 2017 22:02:08 -0500 Subject: py-deeptools: new package and dependencies (#4717) * py-deeptools: new package and dependencies * py-deeptools: fixing python things * missed a fix --- .../repos/builtin/packages/bcftools/package.py | 2 + .../repos/builtin/packages/py-deeptools/package.py | 45 ++++++++++++++++++++++ .../repos/builtin/packages/py-py2bit/package.py | 36 +++++++++++++++++ .../repos/builtin/packages/py-pybigwig/package.py | 37 ++++++++++++++++++ .../repos/builtin/packages/py-pysam/package.py | 39 +++++++++++++++++++ 5 files changed, 159 insertions(+) create mode 100644 var/spack/repos/builtin/packages/py-deeptools/package.py create mode 100644 var/spack/repos/builtin/packages/py-py2bit/package.py create mode 100644 var/spack/repos/builtin/packages/py-pybigwig/package.py create mode 100644 var/spack/repos/builtin/packages/py-pysam/package.py diff --git a/var/spack/repos/builtin/packages/bcftools/package.py b/var/spack/repos/builtin/packages/bcftools/package.py index 6a276709ef..6555692fab 100644 --- a/var/spack/repos/builtin/packages/bcftools/package.py +++ b/var/spack/repos/builtin/packages/bcftools/package.py @@ -39,6 +39,8 @@ class Bcftools(Package): depends_on('zlib') depends_on('bzip2', when="@1.4:") + # build fails without xz + depends_on('xz', when="@1.4") def install(self, spec, prefix): make("prefix=%s" % prefix, "all") diff --git a/var/spack/repos/builtin/packages/py-deeptools/package.py b/var/spack/repos/builtin/packages/py-deeptools/package.py new file mode 100644 index 0000000000..e4e1ec2583 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-deeptools/package.py @@ -0,0 +1,45 @@ +############################################################################## +# 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 NOTICE and LICENSE files 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 PyDeeptools(PythonPackage): + """deepTools addresses the challenge of handling the large amounts of data + that are now routinely generated from DNA sequencing centers.""" + + homepage = "https://pypi.io/packages/source/d/deepTools" + url = "https://pypi.io/packages/source/d/deepTools/deepTools-2.5.2.tar.gz" + + version('2.5.2', 'ba8a44c128c6bb1ed4ebdb20bf9ae9c2') + + depends_on('python@2.7:', type=('build', 'run')) + depends_on('py-setuptools', type='build') + depends_on('py-numpy@1.9.0:', type=('build', 'run')) + depends_on('py-scipy@0.17.0:', type=('build', 'run')) + depends_on('py-py2bit@0.2.0:', type=('build', 'run')) + depends_on('py-pybigwig@0.2.1:', type=('build', 'run')) + depends_on('py-pysam@0.8.2:', type=('build', 'run')) + depends_on('py-matplotlib@1.4.0:', type=('build', 'run')) + depends_on('py-numpydoc@0.5:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-py2bit/package.py b/var/spack/repos/builtin/packages/py-py2bit/package.py new file mode 100644 index 0000000000..d48fb7e9b9 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-py2bit/package.py @@ -0,0 +1,36 @@ +############################################################################## +# 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 NOTICE and LICENSE files 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 PyPy2bit(PythonPackage): + """A package for accessing 2bit files using lib2bit.""" + + homepage = "https://pypi.python.org/pypi/py2bit" + url = "https://pypi.io/packages/source/p/py2bit/py2bit-0.2.1.tar.gz" + + version('0.2.1', 'eaf5b1c80a0bbf0b35af1f002f83a556') + + depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-pybigwig/package.py b/var/spack/repos/builtin/packages/py-pybigwig/package.py new file mode 100644 index 0000000000..4d96ba58c0 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-pybigwig/package.py @@ -0,0 +1,37 @@ +############################################################################## +# 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 NOTICE and LICENSE files 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 PyPybigwig(PythonPackage): + """A package for accessing bigWig files using libBigWig.""" + + homepage = "https://pypi.python.org/pypi/pyBigWig" + url = "https://pypi.io/packages/source/p/pyBigWig/pyBigWig-0.3.4.tar.gz" + + version('0.3.4', '8e0a91e26e87eeaa071408a3a749bfa9') + + depends_on('py-setuptools', type='build') + depends_on('curl', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-pysam/package.py b/var/spack/repos/builtin/packages/py-pysam/package.py new file mode 100644 index 0000000000..cf470ea564 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-pysam/package.py @@ -0,0 +1,39 @@ +############################################################################## +# 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 NOTICE and LICENSE files 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 PyPysam(PythonPackage): + """A python module for reading, manipulating and writing genomic data + sets.""" + + homepage = "https://pypi.python.org/pypi/pysam" + url = "https://pypi.io/packages/source/p/pysam/pysam-0.11.2.2.tar.gz" + + version('0.11.2.2', '56230cd5f55b503845915b76c22d620a') + + depends_on('py-setuptools', type='build') + depends_on('py-cython@0.21:', type='build') + depends_on('bcftools') -- cgit v1.2.3-70-g09d2