dbcreator FAQ

* How do I install databases for multiple organism?

Simply re-run the dbcreator* modules and designate a different organism code with the -g argument.

* Can I run the dbcreator modules on partially completed database?

Yes, the dbcreator* modules skip GFs that have already been installed.

* The dbcreator modules take long time to run. Can I terminate them?

Yes, and you can restart them later. The dbcreator* modules flags partially completed GFs with a '.temp' extension. These GFs are not visible to the server module, and will be installed correctly upon next dbcreator* runs.

* Can I download individual GFs?

Individual GFs can be installed by providing their comma-separated names after the -f parameter (i.e -f knownGene).

Can I simply download all regulatory datasets and let the `dbcreator` modules work with them?

In fact, this is the recommended way. rsync can be used to mirror the USCS data files. Simply create [dir]/downloads/ folder and execute the following command within it:

rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/* .

Remember that rsync is not infallible. To automatically restart broken transfers, check GenomeRunner' source code for autorsync.sh script in the commandline folder.