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transabyss: new package (#4892)

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* transabyss: new package and dependencies

* fixed build deps in igraph and version conflict spec in abyss

* fixed versioning stuff and package structure

*  fixed dep type

* fixing dep type for real this time
This commit is contained in:
Audrey Thoma 2017-08-07 15:42:49 -05:00 committed by Adam J. Stewart
parent 82463f1fd6
commit 825c3c68a3
4 changed files with 123 additions and 2 deletions
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6
var/spack/repos/builtin/packages/abyss/package.py
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@ -31,12 +31,14 @@ class Abyss(AutotoolsPackage):
is useful for assembling genomes up to 100 Mbases in size."""
homepage = "http://www.bcgsc.ca/platform/bioinfo/software/abyss"
url = "http://www.bcgsc.ca/platform/bioinfo/software/abyss/releases/2.0.2/abyss-2.0.2.tar.gz"
url = "https://github.com/bcgsc/abyss/archive/2.0.2.tar.gz"
version('2.0.2', '1623f55ad7f4586e80f6e74b1f27c798')
version('1.5.2', '10d6d72d1a915e618d41a5cbbcf2364c')
depends_on('mpi')
depends_on('boost@:1.50.0,1.53.0:')
depends_on('boost@:1.50.0,1.53.0:', when='@2.0.2:')
depends_on('boost@:1.50.0,1.53.0:1.59.0', when='@:1.5.2')
depends_on('sparsehash')
depends_on('sqlite')

36
var/spack/repos/builtin/packages/igraph/package.py Normal file
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@ -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 Igraph(AutotoolsPackage):
"""igraph is a library for creating and manipulating graphs."""
homepage = "http://igraph.org/"
url = "https://github.com/igraph/igraph/releases/download/0.7.1/igraph-0.7.1.tar.gz"
version('0.7.1', '4f6e7c16b45fce8ed423516a9786e4e8')
depends_on('libxml2')

38
var/spack/repos/builtin/packages/py-igraph/package.py Normal file
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@ -0,0 +1,38 @@
##############################################################################
# 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 PyIgraph(PythonPackage):
"""igraph is a collection of network analysis tools with the emphasis on
efficiency, portability and ease of use."""
homepage = "http://igraph.org/"
url = "http://igraph.org/nightly/get/python/python-igraph-0.7.0.tar.gz"
version('0.7.0', '32a3238cb9041b1686d7d0ba152235bf')
depends_on('py-setuptools', type='build')
depends_on('igraph')

45
var/spack/repos/builtin/packages/transabyss/package.py Normal file
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@ -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 Transabyss(Package):
"""De novo assembly of RNAseq data using ABySS"""
homepage = "http://www.bcgsc.ca/platform/bioinfo/software/trans-abyss"
url = "http://www.bcgsc.ca/platform/bioinfo/software/trans-abyss/releases/1.5.5/transabyss-1.5.5.zip"
version('1.5.5', '9ebe0394243006f167135cac4df9bee6')
depends_on('abyss@1.5.2')
depends_on('python@2.7.6:', type=('build', 'run'))
depends_on('py-igraph@0.7.0:', type=('build', 'run'))
depends_on('blat')
def install(self, spec, prefix):
install('transabyss', prefix)
install('transabyss-merge', prefix)
install_tree('bin', prefix.bin)
install_tree('utilities', prefix.utilities)