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  • Jan 31 2019 17:58
    jorgemachucav starred galaxyproject/tools-iuc
  • Jan 31 2019 17:45
    bebatut opened #2270
  • Jan 31 2019 16:18
    cpreviti synchronize #2267
  • Jan 31 2019 14:15
    cpreviti synchronize #2267
  • Jan 31 2019 12:42
    bernt-matthias review_requested #2269
  • Jan 31 2019 12:42
    bernt-matthias edited #2269
  • Jan 31 2019 12:41
    bernt-matthias edited #2269
  • Jan 31 2019 12:40
    bernt-matthias synchronize #2269
  • Jan 31 2019 12:13
    cpreviti commented #2267
  • Jan 31 2019 12:07
    nsoranzo commented #2267
  • Jan 31 2019 12:01
    cpreviti synchronize #2267
  • Jan 31 2019 11:21
    cpreviti synchronize #2267
  • Jan 31 2019 09:47
    cpreviti synchronize #2267
  • Jan 31 2019 09:27
    cpreviti synchronize #2267
  • Jan 30 2019 20:38
    bernt-matthias commented #2131
  • Jan 30 2019 20:19
    hepcat72 commented #2239
  • Jan 30 2019 19:50
    lparsons commented #2239
  • Jan 30 2019 18:36
    bgruening commented #2268
  • Jan 30 2019 15:23
    nsoranzo commented #2268
  • Jan 30 2019 15:23
    nsoranzo commented #2267
bgruening
@bgruening:matrix.org
[m]
7 you can select and it is shp file
Yvan Le Bras
@yvanlebras
hmm
bgruening
@bgruening:matrix.org
[m]
no
you have uploaded a collection
Yvan Le Bras
@yvanlebras
true... but unfortunately I think this was a very old test of shapefile upload before we created the shapefile composite datatype
bgruening
@bgruening:matrix.org
[m]
but not a composite datatype as it looks like
Yvan Le Bras
@yvanlebras
Ah yes ! Got it !! THANK YOU SO MUCH
bgruening
@bgruening:matrix.org
[m]
?
Yvan Le Bras
@yvanlebras
IN fact this is because it is an old history where we made several tests to upload shapefile data! And this was before having this wonderfull shp composite datatype !
bgruening
@bgruening:matrix.org
[m]
did we solved it?
Yvan Le Bras
@yvanlebras
Now, when I upload a shp composite datafile, I see it on the ogr2ogr tool input parameter !
Youhouhou
Thank you !!!!!!!
Amazing
bgruening
@bgruening:matrix.org
[m]
cool
pvanheus
@pvanheus
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
M Bernt
@bernt-matthias:matrix.org
[m]
With the API key you don't need to specify a user. Galaxy will know which user belongs to the API key.
pvanheus
@pvanheus
ah ok...
Simon Bray
@simonbray:matrix.org
[m]
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
pvanheus
@pvanheus
ah ok thanks!
and do I need to tell it to use the external_galaxy engine?
Simon Bray
@simonbray:matrix.org
[m]
No
But it will probably be a lot faster to point it towards a server, since you can skip tool installation
but then you can only update the workflow to at most the latest version of the tools which are installed on that server
pvanheus
@pvanheus
yep... and that's fine by me
Simon Bray
@simonbray:matrix.org
[m]
👍️
Are you reading the planemo documentation atm or something else? Maybe I can write a few lines extra explanation
pvanheus
@pvanheus
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
Simon Bray
@simonbray:matrix.org
[m]
Ah sorry 😓
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
pvanheus
@pvanheus
and does this rely on a particular Galaxy API version?
seems it doesn't work with a 21.01 server
Simon Bray
@simonbray:matrix.org
[m]
Yes, it requires 21.05
kenza12
@kenza12
Hi, can someone else review this PR : galaxyproject/tools-iuc#4560 in order to merge it ? Thank you !!
Anton Nekrutenko
@nekruten:matrix.org
[m]
Do we any new policy for specifying tool onthology within the wrapper in order to feel the new tool panel?
Nicola Soranzo
@nsoranzo:matrix.org
[m]

You can use:

    <xrefs>
        <xref type="bio.tools">orfipy</xref>
    </xrefs>

which will point to https://bio.tools/orfipy

pvanheus
@pvanheus
sorry, this is news to me - how are xrefs used in the new tool panel?
and should we thus be adding them for every tool?
Helena
@hexylena:matrix.org
[m]
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 :)
Nicola Soranzo
@nsoranzo:matrix.org
[m]
If the tool is on https://bio.tools/ , IUC recommends to add a bio.tools xref, which should provide the EDAM ontology xrefs automagically.
Yvan Le Bras
@yvanlebras
Hi everyone,
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
Helena
@hexylena:matrix.org
[m]
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
Marius
@mvdbeek:matrix.org
[m]
I assume there's more to it ?
pvanheus
@pvanheus
hey there... for our IRIDA deploys we need to have Singularity images - on Galaxy servers these are either (1) pulled from quay.io using the mulled_singularity resolver or (2) (for non-IUC tools) built using the build_mulled_singularity resolver (which actually doesn't work for me at the moment). how can this functionality be run on the command line or via API so that I can get the Singularity images for IUC tools (or potentially for non IUC tools) without running things through a Galaxy server?