toil.utils.toilDebugFile

Debug tool for copying files contained in a toil jobStore.

Module Contents

Functions

fetchJobStoreFiles(jobStore, options)

Takes a list of file names as glob patterns, searches for these within a

printContentsOfJobStore(job_store[, job_id])

Fetch a list of all files contained in the job store if nameOfJob is not

main()

Attributes

logger

toil.utils.toilDebugFile.logger
toil.utils.toilDebugFile.fetchJobStoreFiles(jobStore, options)[source]

Takes a list of file names as glob patterns, searches for these within a given directory, and attempts to take all of the files found and copy them into options.localFilePath.

Parameters:

  • jobStore (toil.jobStores.fileJobStore.FileJobStore) – A fileJobStore object.

  • options.fetch – List of file glob patterns to search for in the jobStore and copy into options.localFilePath.

  • options.localFilePath – Local directory to copy files into.

  • options.jobStore – The path to the jobStore directory.

  • options (argparse.Namespace)

Return type:

None

toil.utils.toilDebugFile.printContentsOfJobStore(job_store, job_id=None)[source]

Fetch a list of all files contained in the job store if nameOfJob is not declared, otherwise it only prints out the names of files for that specific job for which it can find a match. Also creates a log file of these file names in the current directory.

Parameters:

  • job_store (toil.jobStores.fileJobStore.FileJobStore) – Job store to ask for files from.

  • job_id (Optional[str]) – Default is None, which prints out all files in the jobStore. If specified, it will print all jobStore files that have been written to the jobStore by that job.

Return type:

None

toil.utils.toilDebugFile.main()[source]
Return type:

None