From 825c3c68a35f49d93ef753fe974d65ac7d1ed42a Mon Sep 17 00:00:00 2001 From: Audrey Thoma Date: Mon, 7 Aug 2017 15:42:49 -0500 Subject: transabyss: new package (#4892) * 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 --- var/spack/repos/builtin/packages/abyss/package.py | 6 ++- var/spack/repos/builtin/packages/igraph/package.py | 36 +++++++++++++++++ .../repos/builtin/packages/py-igraph/package.py | 38 ++++++++++++++++++ .../repos/builtin/packages/transabyss/package.py | 45 ++++++++++++++++++++++ 4 files changed, 123 insertions(+), 2 deletions(-) create mode 100644 var/spack/repos/builtin/packages/igraph/package.py create mode 100644 var/spack/repos/builtin/packages/py-igraph/package.py create mode 100644 var/spack/repos/builtin/packages/transabyss/package.py (limited to 'var') diff --git a/var/spack/repos/builtin/packages/abyss/package.py b/var/spack/repos/builtin/packages/abyss/package.py index e8e0fb4d45..f3a9f27748 100644 --- a/var/spack/repos/builtin/packages/abyss/package.py +++ b/var/spack/repos/builtin/packages/abyss/package.py @@ -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') diff --git a/var/spack/repos/builtin/packages/igraph/package.py b/var/spack/repos/builtin/packages/igraph/package.py new file mode 100644 index 0000000000..030ef1f604 --- /dev/null +++ b/var/spack/repos/builtin/packages/igraph/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 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') diff --git a/var/spack/repos/builtin/packages/py-igraph/package.py b/var/spack/repos/builtin/packages/py-igraph/package.py new file mode 100644 index 0000000000..7d9c408678 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-igraph/package.py @@ -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') diff --git a/var/spack/repos/builtin/packages/transabyss/package.py b/var/spack/repos/builtin/packages/transabyss/package.py new file mode 100644 index 0000000000..10ee508899 --- /dev/null +++ b/var/spack/repos/builtin/packages/transabyss/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 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) -- cgit v1.2.3-70-g09d2