CHARLIE wrapper fails with conda initialization error on v0.11

[kopardev]

Description

A bioinformatician from HAMB is unable to run the CHARLIE pipeline. The wrapper script (v0.11) fails with conda-related errors.

Error Message

charlie
/data/CCBR_Pipeliner/Pipelines/CHARLIE/v0.11/bin/charlie: line 20: /data/CCBR_Pipeliner/db/PipeDB/Conda/etc/profile.d/conda.sh: No such file or directory

CondaError: Run 'conda init' before 'conda activate'

[+] Loading singularity  4.3.7  on cn0113 
[+] Loading snakemake  7.32.4

Affected Version

• CHARLIE v0.11

Steps to Reproduce

1. Run the charlie command with a dataset
2. Observe the conda initialization failure

Context

• User: Bioinformatician from HAMB
• Lab: Dr. Ziegelbauer's lab
• Issue: The wrapper appears to be outdated and doesn't work with current conda configuration
• The conda.sh initialization script is not found at the expected path: /data/CCBR_Pipeliner/db/PipeDB/Conda/etc/profile.d/conda.sh

Expected Behavior

The CHARLIE pipeline should initialize conda properly and activate the required environments without errors.

[kopardev]

Fixed in v0.13.0: Migrated the runtime conda/mamba activation in the charlie wrapper to a mamba-safe flow that no longer depends on the missing /data/CCBR_Pipeliner/db/PipeDB/Conda/etc/profile.d/conda.sh path. See CHARLIE v0.13.0 release.