Modules folder

[MichielPerneel]

Hi, I wanted to try out a Eukrhythmic test run (snakemake -n) after I pulled to project from github. It throws the following error:

As this folder isn't in the project directory by default, is this something the user should create and subsequently add the .smk rules for the assemblers of interest?

Kind regards, Michiel

[akrinos]

Hi @MichielPerneel !

So we recently changed the organization of the repository such that the modules folder has been renamed rules. This should be changed elsewhere in the repository, it's just that using snakemake -n is currently defunct in eukrhythmic because that runs the Snakefile by default. You could run snakemake -n -s eukrhythmic to run the Snakefile with the non-standard name (eukrhythmic) in the base directory.

However, the best way to run eukrhythmic, even with the -n flag, is using the provided runscripts. You can either use the shell script, by calling it directly or running:

alias eukrhythmic='./bin/eukrhythmic.sh'

and then calling eukrhythmic --dry-run, or you can use the Python run script, by calling:

python submit/eukrhythmic all -np

I will fix the issue of having a defunct default-labeled Snakefile in the base directory - thanks for raising that! Please let me know if the above approaches don't work for you, and of course please continue to keep us updated as you are testing the software (thanks!).

Arianna

[MichielPerneel]

Hi @akrinos, thanks for the quick reply!

Both solutions evoke the checkrequirements.py script at some point, resulting in the file not found error due to the late modules/ folder. I'll try a regular run and see whether I get that up and running!

Also, in the eukrhythmic.sh script I needed to modify lines 45 and 54 (added ;; to the case in --subroutine statements)

[akrinos]

Hi @MichielPerneel , thanks for continuing with this!!

The checkrequirements.py file is in the scripts folder. When import checkrequirements is called within any eukrhythmic script, it should be after the scripts folder is added to the path. Would you mind printing the backtrace you get?

Thanks!

[MichielPerneel]

This is the backtrace of the error:

[akrinos]

Hi @MichielPerneel, can you pull from the repo and try again? :) That script was updated on the branch I am working on, but appears not to have made it to the main branch! Just made a pull request and merged in changes.