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galaxyproject / tools-iuc

Tool Shed repositories maintained by the Intergalactic Utilities Commission
https://galaxyproject.org/iuc
MIT License
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Error tl.paga with Scanpy #3119

Open bellenger-l opened 4 years ago

bellenger-l commented 4 years ago

Hello !

I encounter an error with your tool Cluster, infer trajectories and embed with scanpy (Galaxy Version 1.4.4.post1+galaxy3) when using it for the option tl.paga. I tried your test-data pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad but it also end with an error...

Here is the used parameters : 

Method used | tl.paga
Key for categorical in the input | paul15_clusters
Use RNA velocity to orient edges in the abstracted graph and estimate transitions? | False
PAGA connectivity model | v1.2
advanced_common |  
Output Log? | True

And you can also see the log file : Galaxy3-[Log_file].txt. I use the log file because it was the only way to obtain a bit of informations about the error.

Can you please help me understand and fix this error ?

Thanks for your time, Lea

bellenger-l commented 4 years ago

Hi again !

It's seems to appear when using the conda version of Scanpy instead of Docker, but I don't understand why... I test cluster_reduce_dimension.xml with planemo, with and without the two following parameters : --biocontainers and --no_conda_auto_init and without them : test 4 and 8 failed.

Why does Scanpy's conda package prevent the wrapper from working properly?

I also tested your plotting tool on the galaxy server using methods related to PAGA (pl.paga, pl.paga_compare and pl.paga_path) without success. I tried to use the parameters given in the plot.xml and I saw that the corresponding tests were either commented or missing, maybe that explains why the tool ended in error? Anyway, I would be happy to help adding these tests as soon as I better understand this tool.

Best, Lea