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  • Jan 31 2019 17:58
    jorgemachucav starred galaxyproject/tools-iuc
  • Jan 31 2019 17:45
    bebatut opened #2270
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    nsoranzo commented #2267
bgruening
@bgruening:matrix.org
[m]
Hey everyone, this PR is a very good opportunity for a first-time contributor: galaxyproject/tools-iuc#4492
if you want to contribute this tool is easy to handle and needs an update
you need to add the missing parameters of the new version
Gulsum Gudukbay Akbulut
@gulsumgudukbay
@bgruening both would be fine. Any application that is used frequently is good for testing how beneficial the support is
Nate Coraor
@natefoo:matrix.org
[m]

I was trying to figure out why most of the tool tests of all versions of Pangolin 3.x fail on usegalaxy.org with:

AttributeError in line 112 of /usr/local/tools/_conda/envs/mulled-v1-72f7a2d4de377591b330113007411515001882bdf41ef6a774876b7e70240654/lib/python3.8/site-packages/pangolin/scripts/pangolearn.smk:
'DecisionTreeClassifier' object has no attribute 'n_features_'
  File "/usr/local/tools/_conda/envs/mulled-v1-72f7a2d4de377591b330113007411515001882bdf41ef6a774876b7e70240654/lib/python3.8/site-packages/pangolin/scripts/pangolearn.smk", line 112, in __rule_pangolearn
  File "/usr/local/tools/_conda/envs/mulled-v1-72f7a2d4de377591b330113007411515001882bdf41ef6a774876b7e70240654/lib/python3.8/site-packages/pangolin/pangolearn/pangolearn.py", line 170, in assign_lineage
  File "/usr/local/tools/_conda/envs/mulled-v1-72f7a2d4de377591b330113007411515001882bdf41ef6a774876b7e70240654/lib/python3.8/site-packages/sklearn/tree/_classes.py", line 922, in predict_proba
  File "/usr/local/tools/_conda/envs/mulled-v1-72f7a2d4de377591b330113007411515001882bdf41ef6a774876b7e70240654/lib/python3.8/site-packages/sklearn/tree/_classes.py", line 395, in _validate_X_predict
  File "/usr/local/tools/_conda/envs/mulled-v1-72f7a2d4de377591b330113007411515001882bdf41ef6a774876b7e70240654/lib/python3.8/concurrent/futures/thread.py", line 57, in run
Exiting because a job execution failed. Look above for error message

Both conda and singularity, and so wanted to see how usegalaxy.eu had fixed it - turns out, it's broken on EU too.

This seems to imply it's an install issue but I suspect reinstalling the deps isn't going to help in this case: cov-lineages/pangolin#427
fwiw I also get the following with pangolin 4.0.5+galaxy1 on EU (I don't have 4.x on .org):
Error: the input query fasta could not be parsed.
Double check your query fasta and that compressed stdin was not passed.
Please enter your fasta sequence file and refer to pangolin usage at: https://cov-lineages.org/pangolin.html for detailed instructions.

Error: the input query fasta could not be parsed.
Double check your query fasta and that compressed stdin was not passed.
Please enter your fasta sequence file and refer to pangolin usage at: https://cov-lineages.org/pangolin.html for detailed instructions.
rm: cannot remove '/data/jwd/main/046/882/46882007/tmp/out.3651279': No such file or directory
rm: cannot remove '/data/jwd/main/046/882/46882007/tmp/err.3651279': No such file or directory
wm75 (Wolfgang Maier)
@wm75:matrix.org
[m]
I've been trying to explain to them why it's not a great idea to switch your scikit-learn version when building models for a given release, but seems they rae not really getting the point :(
That's for your 3.1.20 question.
Older models installed via a DM are working still.
wm75 (Wolfgang Maier)
@wm75:matrix.org
[m]
Regarding the v4 series, there should be 4.0.5+galaxy2 in the toolshed already (not sure why it didn't get installed on .eu over the weekend), which addresses a few issues. Your error message really looks like something's wrong with your FASTA input though. If not, then what were the exact parameters you've been using?
Nate Coraor
@natefoo:matrix.org
[m]
I was running the tool tests using galaxy-tool-test
kenza12
@kenza12
Hi, I opened this PR to update rpbasicdesign tool : https://github.com/brsynth/tools-iuc/pull/new/rpbasicdesign_update_1_1_0 . Can anyone review/merge it please ? I also opened this PR (galaxyproject/tools-iuc#4458) for another tool (dnabot) and it was merged but I can't find it in the toolshed . Can you check what's wrong please? Thank you for your work.
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 !