Galactic Radio Telescope

This is an opt-in service which Galaxy admins can configure to contribute their job run data back to the community. We hope that by collecting this information we can build accurate models of tool CPU/memory/time requirements. In turn, admins will be able to use this analyzed data to optimize their job distribution across highly heterogeneous clusters.

Registration

You will need to register your Galaxy instance with the Galactic Radio Telescope (GRT). This can be done https://telescope.galaxyproject.org.

About the Script

Once you’ve registered your Galaxy instance, you’ll receive an instance ID and an API key which are used to run scripts/grt/export.py. The tool itself is very simple to run. GRT will run and produce a directory of reports that can be synced with the GRT server. Every time it is run, GRT only processes the list of jobs that were run since the last time it was run. On first run, GRT will attempt to export all job data for your instance which may be very slow depending on your instance size. We have attempted to optimize this as much as is feasible.

Data Privacy

All data submitted to the GRT will be released into the public domain. If there are certain tools you do not want included, or certain parameters you wish to hide (e.g. because they contain API keys), then you can take advantage of the built-in sanitization. scripts/grt/grt.yml.sample file allows you to build up sanitization for the job logs.

sanitization:
    # Blacklist the entire tool from appearing
    tools:
        - __SET_METADATA__
        - upload1
    # Or you can blacklist individual parameters from being submitted, e.g. if
    # you have API keys as a tool parameter.
    tool_params:
        # Or to blacklist under a specific tool, just specify the ID
        some_tool_id:
            - dbkey
            # If you need to specify a parameter multiple levels deep, you can
            # do that as well. Currently we only support blacklisting via the
            # full path, rather than just a path component. So everything under
            # `path.to.parameter` will be blacklisted.
            - path.to.parameter
            # However you could not do "parameter" and have everything under
            # `path.to.parameter` be removed.
            # Repeats are rendered as an *, e.g.: repeat_name.*.values

To blacklist the results from specific tools appearing in results, just add the tool ID under the tools list.

Blacklisting tool parameters is more complex. In a key under the tool_params key, supply a list of parameters you wish to blacklist. NB: This will slow down processing of records associated with that tool. Selecting keys is done identically to writing test cases, except if you have a repeat element, just replace the location of the numeric identifier with *, e.g. repeat_name.*.some_subkey

Data Collection Process

cd $GALAXY; python scripts/grt/export.py -l debug

export.py connects to your galaxy database and makes queries against the database for three primary tables:

  • job
  • job_parameter
  • job_metric_numeric

these are exported with very little processing, as tabular files to the GRT reports directory, $GALAXY/reports/. We only collect new job data that we have not seen since the previous run. The last-seen job ID is stored in $GALAXY/reports/.checkpoint. Once the files have been exported, they are put in a compressed archive, and some metadata about the export process is written to a json file with the same name as the report archive.

You may wish to inspect these files to be sure that you’re comfortable with the information being sent.

Once you’re happy with the data, you can submit it with the GRT submission tool…

Data Submission

cd $GALAXY; python scripts/grt/upload.py

scripts/grt/upload.py is a script which will submit your data to the configured GRT server. You must first be registered with the server which will also walk you through the setup process.

With your reports, submitting them is very simple. The script will login to the server and determine which reports the server does not have yet. Then it will begin uploading those.

For administrators with firewalled galaxies and no internet access, if you are able to exfiltrate your files to somewhere with internet, then you can still take advantage of GRT. Alternatively you can deploy GRT on your own infrastructure if you don’t want to share your job logs.