Unable to run
GuiSeSanz opened this issue · comments
Hello, I wanted to use the package to filter a bam file by cellBarcode. I installed the package via pip, as in the intructions, bu I encounter the following error...
/Library/Developer/CommandLineTools/usr/bin/python3: No module named sinto.__main__; 'sinto' is a package and cannot be directly executed
what is the command you are running?
Hi!
I installed sinto in an HPC with the command without problems:
pip install --prefix=$PYTHON_LIBS sinto
And when trying to run it as on the documentation, just by tiping sinto, I encounter the dreaded
bash: sinto: command not found
and If I run it with this command, I encounter the message above
python3 -m sinto
/sw/rl9c/python/3.11.0/rl9_gnu12.2.0/bin/python3: No module named sinto.__main__; 'sinto' is a package and cannot be directly executed
Ok, sinto cannot be run using python -m sinto you would need to use the sinto command on the command line. It looks like this could be a path issue, you should make sure you have the python paths set up correctly
Ok, I'm trying to solve it...
When I explore the path where all the python libraries are installed, I'm able to locate sinto, in
XXX/local/python3.11.0_gnu12.2.0_libs/lib/python3.11/site-packages/sinto
This folder contains several scripts (see below), but I cannot see a main script or anything, Is there a way to launch it from here?
addbarcodes.py addtags.py arguments.py blocks.py cli.py constants.py filterbarcodes.py fragments.py __init__.py __pycache__ tagtoname.py tagtorg.py tagtotag.py utils.py
Also, python3 cli.py yields no result or message...
My guess is that you need to update your path with the path to the python installation directory. For you it could be something like XXX/local/python3.11.0_gnu12.2.0_libs/lib/python3.11/bin/sinto, but I'm not sure
FYI, we use python entry points to run the main function in arguments.py by calling sinto on the command line https://github.com/timoast/sinto/blob/master/setup.cfg#L27-L29. Calling individual scripts within the package like cli.py won't help..
Ok! Thank you very much for your help! since the issue is no longer related to the library, I'll close the issue!
Thanks again!