help with setting up and running

[shobhitagrawal1]

Dear Felix,
Thank you for the great tool, it can really help in my current endeavour of defining de-novo cell types for atlas level data, which has several covariates. I am trying to install and run the program, however, running into some problems.
My current strategy was to download the smsh file provided by you and then convert it to a singularity container and then run the program.
I assumed, perhaps incorrectly that the cellnet module will be available in the container, however, I could not import it.
Trying to install from pip after cloning also failed, owing to container permissions. I can of course try other ways including creating a sandbox etc.
I would be really happy if you could just give me some tips regarding how to get the program up and running starting from downloading the smsh file, converting to a singularity container.
I am sorry to bother you and apologize for a noob question.
Thanking you
shobhit

[felix0097]

Hi shobhit,

yes the module is not installed in the container. But you should be able to install it via pip install -e . --no-deps (You don't need to install any dependencies, they're already installed in the container image).

Let me know if that works for you,
Felix

[shobhitagrawal1]

thanks for the promot reply. i will try again tonight!