Conda environment for read density estimation cannot activate

[TBradley27]

Hey,

With this repo, I am trying to estimate read densities by setting estimateReadDensity = True in config/config.yaml

The repo works fine when estimateReadDensity = False , but when it is set to True, we get an error message relating to conda environments. This is the full error message:

Conda must be version 24.7.1 or later, found version 23.11.0. Please update conda to the latest version. 

Note that you can also install conda into the snakemake environment without modifying your main conda installation.

I have had a look, and 23.11.0 is the conda version installed in the scAbsolute container image (v3.8.0) tested with the most recent commit at the time of writing - b60d97b. I imagine that what is happening is that this conda version conflicts with minimal dependencies needed to construct the conda environment specified in the postition search yaml file

This bug was discovered by Jao Chong (@Jaoseph), a new research assistant in the Brenton group

[shafighi]

Hi,

Thanks for reporting this issue.
Could you please share the Conda version in your Snakemake environment?

[Jaoseph]

Hi,

The conda version currently installed for the snakemake environment is Conda 24.11.3.

[Lesky47]

Hi, I'm having the same issue where snakemake v8.30 requires conda 24.7.1+, but scAbsolute container image has builtin version 23.11.0. Is there a quick fix to get it solved? I have tried to bind my system conda to the container but it still failed. Thanks!