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Youhouhou
Thank you !!!!!!!
Amazing
I'm trying to make sense of how to use
planemo autoupdate - if I just run it locally it times out trying to install tools... so I'd like to use the --profile option... but I don't understand how profiles work... they seem to need a Galaxy URL and Galaxy user or admin API key... but I don't see where the Galaxy user is specified. Or what the database stuff is for
With the API key you don't need to specify a user. Galaxy will know which user belongs to the API key.
Hey @pvanheus I don't think you need to use a profile. It should be enough to append
--galaxy_url URL --galaxy_user_key API_KEY to the command
and do I need to tell it to use the external_galaxy engine?
but then you can only update the workflow to at most the latest version of the tools which are installed on that server
Are you reading the planemo documentation atm or something else? Maybe I can write a few lines extra explanation
planemo documentation... this section: https://planemo.readthedocs.io/en/latest/autoupdate.html#updating-workflows
so I tried
planemo autoupdate --galaxy_url http://blah --galaxy_user_key blah workflow.ga with planemo 0.74.9 and it doesn't recognise the galaxy_url flag
I was wrong, it seems you have to use a profile. Probably that should be changed since it seems people generally prefer to enter URL and API key directly
planemo profile_create my_new_profile --galaxy_url http://blah --galaxy_user_key
and then
planemo autoupdate workflow.ga --profile my_new_profile
seems it doesn't work with a 21.01 server
Hi, can someone else review this PR : galaxyproject/tools-iuc#4560 in order to merge it ? Thank you !!
Do we any new policy for specifying tool onthology within the wrapper in order to feel the new tool panel?
You can use:
<xrefs>
<xref type="bio.tools">orfipy</xref>
</xrefs>which will point to https://bio.tools/orfipy
and should we thus be adding them for every tool?
they're used for fetching the edam terms, which are then used to make the nice edam based categories in the alternative views of the panel
definitely please add them :)
If the tool is on https://bio.tools/ , IUC recommends to add a
bio.tools xref, which should provide the EDAM ontology xrefs automagically.
Hope all is ok on your sides
We are looking at creating tools who need to take as input couples of datafile and related metadata file, and this is manage for now using file names. I don't find good info / doc on how t omanage input data file names and so on so we can be sure to have ths good "links" between data and related metadata if users select multiple files as input....
4 replies
https://github.blog/2022-05-09-supercharging-github-actions-with-job-summaries/ maybe would be nice for tool testing reports, we could have more detail directly visible and not requiring download