Question: Making Changes to Data Tables in Tools
gravatar for marcoalbuquerque.sfu
3.3 years ago by
marcoalbuquerque.sfu50 wrote:

Lets say I wanted to have a tool that would install a genome and annotation information. And lets say that this tool automatically added entries to the packages data table.

Would this data table need to be reloaded? In other words, would the galaxy instance need to be rebooted for the user to run other tools that use the this data table (rather, the new entry just added to the data table)?


ADD COMMENTlink modified 3.2 years ago by Jennifer Hillman Jackson25k • written 3.3 years ago by marcoalbuquerque.sfu50

If it helps, here is a further explanation of exactly what I am trying to do.

From what I know, data tables require manual setup before being able to use them. It would be really cool if there were ways to add new data entries to the table, automatically, within tools. Why? Some references are more suited to be stored in a directory and not as a single file (i.e. aren't really passable as galaxy inputs). some examples include ensembl vep annotation references, snap aligner references, etc.

What I want the user to be able to do is download a genome using ensembl installer automatically. This entry would then be added to some data table. This data would persist somewhere on the Galaxy filesystem.

Currently I have this working but genomes are installed to Ensembl Install Directory, and I must create a table of all possible genomes offered by Ensembl (i.e. the list does not dynamically change as the user installs a genome).

There are alot of different indexes for the variety of tools I am adding to galaxy, Just seems like alot of work to enforce the user sets up all these different tables, and if we could just create the index in Galaxy, and store them somewhere, it would be really user friendly.

Please let me know if you have any advice on this. Thanks.


ADD REPLYlink written 3.2 years ago by marcoalbuquerque.sfu50
gravatar for Jennifer Hillman Jackson
3.2 years ago by
United States
Jennifer Hillman Jackson25k wrote:


Creating a Data Manager to do the data installation is the recommended method for this work. See the current examples in the Tool Shed to understand more about how these function. A restart would be needed.

Another option is to design the tools so that they use data as direct inputs. These data could be placed into a Data Library where all users have access. 

Other alternatives from the community are welcomed, Jen, Galaxy team

ADD COMMENTlink written 3.2 years ago by Jennifer Hillman Jackson25k

This is exactly what I wanted!

Thanks so much.

ADD REPLYlink written 3.2 years ago by marcoalbuquerque.sfu50
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