Closed dr-joe-wirth closed 1 year ago
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.
I think the issue is the command. Try PhiSpy.py
instead of phispy
.
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!
I installed using
conda install -c bioconda psispy
. But runningphispy
produced the following error:I fixed the error by modifying the
phispy
file:os
PhiSpy.py
to the path usingsys
andos
:sys.path.insert(0,os.path.join(sys.path[0], '<path>/miniconda3/envs/phispy/bin'))
from PhiSpy.py import main
tofrom PhiSpy import main
sys.argv
was not being passed tomain
at the end of the file. So I modified the line fromsys.exit(main())
tosys.exit(main(sys.argv))
These changes allowed the command
phispy
to work