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Publish PGDB on GitHub?

asked 2018-12-16 03:08:03 -0500

rpelicae gravatar image


Is it possible to publish a PGDB of a microorganism on a GitHub project account as part of a genome-scale metabolic reconstruction project? This would mean that the packaged version of the PGDB would be available in a GitHub repository with public access enabled.

If yes, how would I need to adapt the workflow for publishing a PGDB in the Registry as described in Chapter 6 of the Pathway Tools manual?

Kind regards,


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answered 2018-12-16 19:57:04 -0500

Suzanne Paley gravatar image

Hi Rudy,

I'm not quite sure what you are asking. If you are asking if you can somehow publish the PGDB through the Registry, but have it stored on and retrieved from GitHub instead of normal registry mechanism (which requires you make it available via an HTTP service), then the answer is no (although it is an interesting idea). If you are just asking if you are allowed to include your PGDB in your GitHub repository, so that others who know to look in your GitHub repository can download it themselves, then the answer is yes. You would just need to tar up the <orgid>cyc directory and make the resulting tar file available. Anyone who wants to use it in their own Pathway Tools distribution would then need to know to untar it and place the resulting directory in their own ptools-local/pgdbs/user/ directory.


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Asked: 2018-12-16 03:08:03 -0500

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Last updated: Dec 16 '18