conda installation failed

[dr-joe-wirth]

I installed using conda install -c bioconda psispy. But running phispy produced the following error:

Traceback (most recent call last):                                                                                                                                         
  File "/scicomp/home-pure/uma2/miniconda3/envs/phispy/bin/phispy", line 7, in <module>                                                                                    
    from PhiSpy.py import main                                                                                                                                             
ModuleNotFoundError: No module named 'PhiSpy.py'; 'PhiSpy' is not a package

I fixed the error by modifying the phispy file:

• I imported os
• I added the directory containg PhiSpy.py to the path using sys and os: sys.path.insert(0,os.path.join(sys.path[0], '<path>/miniconda3/envs/phispy/bin'))
• I changed the import statement from from PhiSpy.py import main to from PhiSpy import main
• Finally, sys.argv was not being passed to main at the end of the file. So I modified the line from sys.exit(main()) to sys.exit(main(sys.argv))

These changes allowed the command phispy to work

[linsalrob]

This should not be necessary, and I don't know why you had to do this. All conda tests currently pass.

Please don't do this, as you will almost certainly break things.

[linsalrob]

I think the issue is the command. Try PhiSpy.py instead of phispy.

[dr-joe-wirth]

Nothing broke. It ran just fine after the fix I mentioned above as it was just telling the phispy file where to look. Plus main in the phispy file was not being invoked properly as sys.argv is a required argument.

If I recall correctly, I had tried running PhiSpy.py but it didn't run. This was last week though and I stopped thinking about it as soon as I posted this issue, so it is possible I am misremembering.

Thanks for following up on this!