Open axiomcura opened 2 years ago
This is also apparent in when trying to use the from cytosnake.utils.config_util
modules. CytoSnake
contains it's own helper functions that parses the config files. However, since CytoSnake
is not included within the conda
environment for each rule, it does not exists. Therefore, I am marking this as a high priority
issue because it is essential that all of CytoSnake
's helper functions are included in each rule.
Here's the error below:
Activating conda environment: .snakemake/conda/b491f577b7124c295ec8a6bb7a1ff3c1_
WARNING:snakemake.logging:Activating conda environment: .snakemake/conda/b491f577b7124c295ec8a6bb7a1ff3c1_
Traceback (most recent call last):
File "/home/erikserrano/tests/cytosnake_tests/test_cp_process_singlecells/.snakemake/scripts/tmp1iylq6h9.convert.py", line 15, in <module>
from cytosnake.guards.ext_guards import has_sqlite_ext
ModuleNotFoundError: No module named 'cytosnake'
As mentioned in #17 the workflow scripts currently do not take imports due to
snakemake's
restrictive design. The issue occurs when declaring an environment withinrules
insnakemake
files.The
snakemake
rules
are entirely encapsulated within the declared evironment file. Sincecytosnake
is not an installable package, then it cannot be installed in the environment therefore not having access tocytosnakes
helper functions.A solution to this is making
cytosnake
making itpip
installable. This will allowcytosnake
to become a required dependency in theconda
environment files, therefore having access to the helper function thatcytosnake
provides.