Galaxy plugin - InterMine

[julie-sullivan]

We have a FlyMine tool right now:

https://github.com/galaxyproject/galaxy/blob/dev/tools/data_source/flymine.xml

We have one for each mine. Looking at that file, it seems like we can replace with info from the registry.

Can we have a generic InterMine tool that will work for any mine in the registry?

Tell @danielabutano @yochannah

[julie-sullivan]

@danielabutano @yochannah Do we have / need docs for this? Can I close this issue?

[danielabutano]

galaxy has NOT released yet the full integration with intermine. I would leave open this issue

[yochannah]

We should also add some guidance to the Galaxy Training network for this before we close it.

…

On Thu, 18 Oct 2018 at 10:59, Daniela Butano ***@***.***> wrote: galaxy has NOT released yet the full integration with intermine. I would leave open this issue — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#1819 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AI14jtTB2lRazRq-cnFDG1HCjnF93e_Kks5umFDWgaJpZM4Ui2kh> .

[danielabutano]

Export data from Intermine to Galaxy
There are 2 options:
1- If you are in a mine instance, for instance flymine, you can run a query, select the option Export -> Send to Galaxy and the data will be exported in the galaxy instance specified in the Galaxy Location field (current implementation).
2- If you are in Galaxy, use the NEW intermine tool to be redirected to the registry, select the InterMine instance you want to use to export the data, run the query, select the option Export -> Send to Galaxy and the data will be exported in the Galaxy instance you started from.
At this purpose, a new endpoint has been implemented in the registry; it receives in input the GALAXY_URL parameter which will be used for the callback
http://registry.intermine.org/im-to-galaxy?GALAXY_URL=https%3A//usegalaxy.org/tool_runner%3Ftool_id%3Dintermine

Export data from from Galaxy to InterMine
You are in Galaxy, you can export data selecting InterMine, then you will be redirected to the registry, where you can select the specific mine where you want to send your Galaxy data.
You will be redirected to the portal page of the mine selected.
At this purpose a new endpoint has been implemented in the registry:
http://registry.intermine.org/galaxy-to-im?URL={url provided by Galaxy to download the file containing type of identifier + identifier}