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Access pipeline working in Ridgeback #74

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Jun 17, 2020
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Access pipeline working in Ridgeback #74

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d2c9a43
initial
aef- May 1, 2020
13f7279
update paths for now
aef- May 13, 2020
6652710
Update jobsubmitter.py
aef- May 15, 2020
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10 changes: 10 additions & 0 deletions submitter/jobsubmitter.py
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Original file line number Diff line number Diff line change
Expand Up @@ -104,6 +104,16 @@ def _prepare_directories(self):
os.mkdir(self.job_tmp_dir)

def _command_line(self):
"""
Start ACCESS-specific code
In addition to different arguments and required bins, ACCESS requires a specific version of Toil that prevents the following PATH from recursively appending itself on every job, causing "OSExit Too many argument".
"""
path = "PATH=/work/access/testing/users/fraihaa/ridgeback/conda/envs/toil-msk-3.21.1-MSK-rc1/bin:/conda/bin:/home/accessbot/miniconda3/envs/ACCESS_1.3.26/bin/:{}".format(os.environ.get('PATH'))
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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@aef- aef- May 1, 2020 •
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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.


command_line = [settings.CWLTOIL, '--singularity', '--logFile', 'toil_log.log', '--batchSystem','lsf','--disable-user-provenance','--disable-host-provenance','--stats', '--debug', '--disableCaching', '--preserve-environment', 'PATH', 'TMPDIR', 'TOIL_LSF_ARGS', 'SINGULARITY_PULLDIR', 'SINGULARITY_CACHEDIR', 'PWD', '--defaultMemory', '8G', '--maxCores', '16', '--maxDisk', '128G', '--maxMemory', '256G', '--not-strict', '--realTimeLogging', '--jobStore', self.job_store_dir, '--tmpdir-prefix', self.job_tmp_dir, '--workDir', self.job_work_dir, '--outdir', self.job_outputs_dir, '--maxLocalJobs', '500']
app_location, inputs_location = self._dump_app_inputs()
if self.resume_jobstore:
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