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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
Yvan Le Bras
@yvanlebras
hope all is ok on your side !
for example, with the ogr2ogr tool, I can't select the dataset 21
bgruening
@bgruening:matrix.org
[m]
21 is a collection
with type binary
so this is corerct that you can not select it
Yvan Le Bras
@yvanlebras
yes, as this is coming from a composite datatype upload
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 :)