Access pipeline working in Ridgeback #74
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aef-
commented
May 1, 2020
submitter/jobsubmitter.py
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| command_line = [path, 'toil-cwl-runner', '--logFile', 'toil_log.log', '--batchSystem','lsf','--disable-user-provenance','--logLevel', 'DEBUG','--disable-host-provenance','--stats', '--debug', '--cleanWorkDir', 'always', '--disableCaching', '--preserve-environment', 'PATH', 'TMPDIR', 'TOIL_LSF_ARGS', 'SINGULARITY_PULLDIR', 'SINGULARITY_CACHEDIR', 'PWD', '_JAVA_OPTIONS', 'PYTHONPATH', 'TEMP', '--defaultMemory', '10G', '--realTimeLogging', '--jobStore', self.job_store_dir, '--tmpdir-prefix', self.job_tmp_dir, '--workDir', self.job_work_dir, '--outdir', self.job_outputs_dir] | ||
| """ | ||
| End ACCESS-specific code | ||
| """ |
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There's no condition, wanted to get feedback as to the preferred approach -- whether I can just check the string of the inputs or filepaths rather than pass a flag in the request param to check whether the job is ACCESS or not. I'm also curious if there's a preference on where to put the bin folders we're passing to PATH.
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I think the cleanest way to implement the condition would be to use the github.repository value using self.app to check for the ACCESS pipeline. This will link the pipeline github repository with that function in ridgeback. I think checking the string of the inputs might cause unintentional collisions.
nikhil
approved these changes
May 15, 2020
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Working version of the ACCESS pipeline in Ridgeback. See comments...
Because ACCESS pipeline is a private repo, and our Git version on Juno is a little outdated, we have to pass the ssh_key when we start the server, it looks something like: