64bdc3251f
- Add a test that verifies checksums on all packages - Also add an attribute to packages that indicates whether they need a manual download or not, and add an exception in the tests for these packages until we can verify them.
84 lines
3.0 KiB
Python
84 lines
3.0 KiB
Python
# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
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# Spack Project Developers. See the top-level COPYRIGHT file for details.
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#
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# SPDX-License-Identifier: (Apache-2.0 OR MIT)
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from spack import *
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from spack.util.environment import EnvironmentModifications
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import os
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class Fsl(Package):
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"""FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI
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brain imaging data.
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Note: A manual download is required for FSL.
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Spack will search your current directory for the download file.
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Alternatively, add this file to a mirror so that Spack can find it.
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For instructions on how to set up a mirror, see
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http://spack.readthedocs.io/en/latest/mirrors.html"""
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homepage = "https://fsl.fmrib.ox.ac.uk"
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url = "file://{0}/fsl-5.0.10-sources.tar.gz".format(os.getcwd())
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manual_download = True
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version('5.0.10', '64823172a08aad679833240ba64c8e30')
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depends_on('python', type=('build', 'run'))
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depends_on('expat')
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depends_on('libx11')
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depends_on('glu')
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depends_on('zlib')
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depends_on('libpng')
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depends_on('boost')
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depends_on('sqlite')
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conflicts('%gcc@6:', when='@5.0.10')
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def patch(self):
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# Uncomment lines in source file to allow building from source
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with working_dir(join_path(self.stage.source_path, 'etc', 'fslconf')):
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sourced = FileFilter('fsl.sh')
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sourced.filter('#FSLCONFDIR', 'FSLCONFDIR')
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sourced.filter('#FSLMACHTYPE', 'FSLMACHTYPE')
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# Fix error in build script
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buildscript = FileFilter('build')
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buildscript.filter('mist-clean', 'mist')
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def install(self, spec, prefix):
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build = Executable('./build')
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build()
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install_tree('.', prefix)
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def setup_environment(self, spack_env, run_env):
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if not self.stage.source_path:
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self.stage.fetch()
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self.stage.expand_archive()
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spack_env.set('FSLDIR', self.stage.source_path)
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# Here, run-time environment variables are being set manually.
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# Normally these would be added to the modulefile at build-time
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# by sourcing fsl.sh, but incorrect paths were being set, pointing to
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# the staging directory rather than the install directory.
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run_env.set('FSLDIR', self.prefix)
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run_env.set('FSLOUTPUTTYPE', 'NIFTI_GZ')
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run_env.set('FSLMULTIFILEQUIT', 'TRUE')
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run_env.set('FSLTCLSH', self.prefix.bin.fsltclsh)
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run_env.set('FSLWISH', self.prefix.bin.fslwish)
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run_env.set('FSLLOCKDIR', '')
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run_env.set('FSLMACHINELIST', '')
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run_env.set('FSLREMOTECALL', '')
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run_env.set('FSLGECUDAQ', 'cuda.q')
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run_env.prepend_path('PATH', self.prefix)
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# Below is for sourcing purposes during building
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fslsetup = join_path(self.stage.source_path, 'etc', 'fslconf',
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'fsl.sh')
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if os.path.isfile(fslsetup):
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spack_env.extend(EnvironmentModifications.from_sourcing_file(
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fslsetup))
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