Question: Making Changes to Data Tables in Tools
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marcoalbuquerque.sfu • 50 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)?
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modified 3.2 years ago
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Jennifer Hillman Jackson ♦ 25k
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3.3 years ago by
marcoalbuquerque.sfu • 50
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.