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Unable to successfully run Slingshot #7
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Hi @matthieubulte, Thank you for bringing this to our attention. So far I've only tested the runSlingshot.py code on Linux and I have not encountered this error before. Could you confirm if you can see a curves.csv file in your output folder under 'Synthetic/mCAD/'? If so, that would mean the docker part of the code has run successfully. As far as I can tell the NSException error is specific to Mac OS. If I understand the issue correctly, it is probably the plotting function here that's causing the issue. Can you try the solution posted here? Let me know if that fixes the issue. Best, |
Hi @adyprat, Yes, the If it works, I'll prepare a PR to add this fix and give the user the option to skip the plotting part. Would it make sense? EDIT: thanks for your answer! |
Sure thing! We plotted the Slingshot output by default for all instances to visualize the computed pseudotime while testing the code. I suppose giving a user option for plotting makes sense. Thank you, |
…abled via a command line argument. Also fixes Murali-group#7
…abled via a command line argument. Also fixes Murali-group#7
Hi!
I'm having issues running the
script-to-generate-datasets.sh
, in particular the pseudo-time inference part.More precisely, when running only the slingshot part of the script, the python script seems to fail after a couple of hours.
Here are the logs
I'm running this on MacOS 10.14.6 with Docker 2.1.0.3.
Please let me know if there is any other information that could be useful to you.
Thanks!
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