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  • Jan 31 2019 17:58
    jorgemachucav starred galaxyproject/tools-iuc
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Yvan Le Bras
@yvanlebras
Hi amazing IUC!
Hope all is ok on your sides !
We are trying to add some conda recipes but tests fails...
If someone has an idea conda-forge/staged-recipes#18967
1 reply
Cristóbal Gallardo
@gallardoalba:matrix.org
[m]
> library('dissUtils') 2022-05-17T07:43:35.5948057Z Error in library("dissUtils") : there is no package called 'dissUtils'
Yvan Le Bras
@yvanlebras
the "final" problem is effectively the env don't find the R packages for which we wrote the recipes... But, locally, testing the recipes with "conda-build" we have a exit 0 code + in the log, loading the libraries are ok....
(the recipes are related to mmand, dissUtils and geometa R packages)
Moreover is there anyone there having created a conda recipe from an archived (outdated) R package?
Yvan Le Bras
@yvanlebras
FYI we fixed our issues with conda recipes ;)
just using https://github.com/bgruening/conda_r_skeleton_helper to generate conda recipe from R package, we have some "extra files" not mandatory normally for proposing a recipe BUT in fact this is mandatory for the github tests to b ok ;)
Another question ;)
concerning the fact we want a tool proposing as input data a composite format, shp.

we wrote this :

<inputs>
        <param type="data" name="input" format="shp,xml,json,tabular,txt"

https://toolshed.g2.bx.psu.edu/repository?repository_id=4127eedef3aaafec

but in fact I see that we can't access shp composite files from the tool (for example on eu: https://ecology.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/ecology/gdal_ogr2ogr/gdal_ogr2ogr/3.0.0)
if you have any information
;)
bgruening
@bgruening:matrix.org
[m]
can you maybe share a history with some example data?
Yvan Le Bras
@yvanlebras
thank you Björn!
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