GenomeComb

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Scientific applications

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Supplementary Data Reumers, De Rijk et al

Genomecomb moved to github on https://github.com/derijkp/genomecomb with documentation on https://derijkp.github.io/genomecomb. For up to date versions, go there. These pages only remain here for the data on the older scientific application (or if someone really needs a long obsolete version of the software)

job_update

Format

cg job_update ?options? logfile ..

Summary

updates the logfile of a command using joboptions

Description

If the logfile of a command using joboptions has the extension .running, the command (or its jobs on a cluster) is either still running or it crashed without being able to update the log. cg job_update can be used to update the log to current status. The status (and times, ...) for each job will be updated. If the command is no longer running, the logfile will get the extension .finished if all jobs were successfully run, and .error if any of them had errors.

Options

-c success/never/allways (-dcleanup)

by default (success) the log_jobs directories containing run, log, error, wtc. files are removed after a successful run, but not after one with errors. never will always keep the job_log dirs, and allways will always remove them. after a succesfull run

-f 0/1 (-force)

use 1 to force aquiring job metadata from log_jobs dirs, even if it already in the logfile

-r 0/1 (-dremoveold)

remove older logfiles, keeping only the last one

Category

Compression