https://usegalaxy.eu status: https://stats.galaxyproject.eu Forum: https://help.galaxyproject.org
@tamannasharma22: do you have access rights to the data behind that link, i.e. can you down load it with your browser without being logged in into an account on the remote server? The error usually means that the remote server responded with some html-formatted error message instead of sending data.
@tamannasharma22: well, that is an html page (look at its source code in your browser) so what Galaxy will receive when you give it that link is the html code, not the data you want.
You either need to locate the underlying data directly at NCBI and get e.g. an ftp link to it, or simpler use this tool https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.7+galaxy0 to download it using its ID.
You either need to locate the underlying data directly at NCBI and get e.g. an ftp link to it, or simpler use this tool https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.7+galaxy0 to download it using its ID.
<del>Is Apply Rules working for others?</del> nvm, eu nonresponsive.
@platuconsina: Mothur tools run on a different/tiny cluster and there is always a long queue. Nothing wrong here
@ToMatschulla: For the Jupyter analysis in Galaxy, the Trajectory Analysis using Python training is recommended, and it uses a pre-clustered scRNA dataset from this Zenodo link
@ToMatschulla : Oh sorry, the input is the AnnData object and the iPynb from the above Zenodo link, specifically:
https://zenodo.org/record/4726927/files/Trajectories_Instructions.ipynb
https://zenodo.org/record/4726927/files/Final_cell_annotated_object.h5ad@ToMatschulla : Oh I see! Yes, so I think as long as you have an AnnData file which has some prior-clustering on it, then you should be able to use that in the trajectory analysis.
For example, I think the AnnData file you generate from the Plant Training should be able to be used in the Trajectory training linked above, and also the output of the "Clustering 3K PBMCs" training should produce an AnnData file you can use for trajectory analysis too.
we don't have infinite resources
ten slots freed, you are on run
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yes
we 10 nodes with ~10 slots each, dedicated to ITs
but if can suggest nicely to kill them if not used, would be great
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not just letting them run forever
nope. now they run until
min(30 days, killed)
but i haven't done anything
and the parameters are the same as I would run this job successfully in the past
@annagias: we can help you if you send us the error report. From the failed step in your history, click on the "bug" button and submit the error report.
