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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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os.getLogin() function breaks seurat.py #250

Open RoganGrant opened 1 year ago

RoganGrant commented 1 year ago

First of all, thank you for this package. It is an essential tool for open science and a serious workhorse for us.

I am currently trying to generate a cellbrowser object from a seurat RDS. However when I run the cbImportSeurat function, it invariably returns the error

OSError: [Errno 6] No such device or address

This appears to result from line 433 of the seurat.py script due to os.getLogin(). This appears to be more of an os issue than anything related to cellbrowser. Indeed, if I run os.getLogin() on the python command line within my current environment I get the same error. Should I try to install glibc on our cluster? Alternatively, would it be possible to substitute this for an equivalent function in a future version?

Thanks for your help!

maximilianh commented 1 year ago

Oops. This line is not important at all. I’ll remove it. Can you temporarily comment it out to make it work for you ?

Thanks for the feedback. I didn’t know it was a problematic function call.

On Wed 3 Aug 2022 at 19:05, Rogan Grant @.***> wrote:

First of all, thank you for this package. It is an essential tool for open science and a serious workhorse for us.

I am currently trying to generate a cellbrowser object from a seurat RDS. However when I run the cbImportSeurat function, it invariably returns the error

OSError: [Errno 6] No such device or address

This appears to result from line 433 of the seurat.py script due to os.getLogin(). This appears to be more of an os issue https://bugs.python.org/issue40821 than anything related to cellbrowser. Indeed, if I run os.getLogin() on the python command line within my current environment I get the same error. Should I try to install glibc on our cluster? Alternatively, would it be possible to substitute this for an equivalent function in a future version?

Thanks for your help!

— Reply to this email directly, view it on GitHub https://github.com/maximilianh/cellBrowser/issues/250, or unsubscribe https://github.com/notifications/unsubscribe-auth/AACL4TOJ6B5C5GZYYTGRVFTVXKREHANCNFSM55PSUHWA . You are receiving this because you are subscribed to this thread.Message ID: @.***>

RoganGrant commented 1 year ago

Wow, thank you for the fast response! Yes I can do that.