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maximilianh / cellBrowser

main repo: https://github.com/ucscGenomeBrowser/cellBrowser/ - Python pipeline and Javascript scatter plot library for single-cell datasets, http://cellbrowser.rtfd.org
https://github.com/ucscGenomeBrowser/cellBrowser/
GNU General Public License v3.0
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R fails silently instead of producing an error code #53

Closed pcm32 closed 5 years ago

pcm32 commented 5 years ago

Here https://github.com/maximilianh/cellBrowser/blob/914bbf5c300203b90072ae3e8c0a0e227708646d/src/cbImportSeurat#L3 R fails silently, without producing an error code, which is normally used in workflow environments/bash pipelines to detect whether a process failed or not. If the code fails, it should exit with an error code (anything not zero). In that line, I think that correct package is argparse and not argparser.

Thanks!

maximilianh commented 5 years ago

Sorry I didn't write this, but also this whole command doesn't really fit into the collection. I wonder if we should replace it with some python code.

maximilianh commented 5 years ago

With your feature requests, I never know if you really need this or if you're just looking at it because it would be nice to have. Are you actually interested in this program for actual use? If you're not using it right now, I'd rather remove it, because we have functions now for source() for Seurat2 and built into Seurat3, so I don't see a use case for this script anymore...

maximilianh commented 5 years ago

Hm, from the fact that you were probably running this in a cluster system, I guess that you are using this? The problem may be that I don't know what are you doing with your internal pipeline system. It seems that you're running many, many things.

pcm32 commented 5 years ago

Sorry I didn't write this, but also this whole command doesn't really fit into the collection. I wonder if we should replace it with some python code.

Well, I'm not sure that you will be able to read an R object from within python, so I guess we are bound to this while we don't have better support for exchange formats (loom, zarr, etc). But if you do find a way, by all means. Maybe you can leave this in a utils or contrib directory where you mention that this is available but that you don't maintain it as such.

With your feature requests, I never know if you really need this or if you're just looking at it because it would be nice to have. Are you actually interested in this program for actual use?

Whenever I ask for something, or I PR it, is because I need it/using it or I intend to use in the near future :-). For instance the seurat part: https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/blob/020b0bcaed4f30a787bfd00995feea9458e902d0/tools/tertiary-analysis/ucsc-cell-browser/cell-browser.xml#L31

maximilianh commented 5 years ago

I am closing this, because now we have the much better tool cbImportSeurat2, which seems to work fine (thanks again for providing a sample file!)