I recently created a Snakemake profile using the guide at Snakemake-Profiles/slurm. I was able to get the profile installed successfully, and it does work when calling the path directly. However, when using the profile name, such as
snakemake --profile slurm --dry-run
I get the error:
Error: profile given but no config.yaml found. Profile has to be given as
either absolute path, relative path or name of a directory available in either
/etc/xdg/snakemake or /home/GROUP/USERNAME/.config/snakemake.
I have indeed installed the profile under ~/.config/snakemake
. Here is the tree of this directory:
/home/GROUP/USERNAME/.config/snakemake
.
└── slurm
├── cluster_config.yaml
├── config.yaml
├── CookieCutter.py
├── __pycache__
│ ├── CookieCutter.cpython-39.pyc
│ └── slurm_utils.cpython-39.pyc
├── settings.json
├── slurm-jobscript.sh
├── slurm-status.py
├── slurm-submit.py
└── slurm_utils.py
2 directories, 10 files
I can continue to specify the path to this profile when running Snakemake, but it would be useful to simply give it the name of the profile. Does anyone happen to know why Snakemake doesn't seem to be picking up that the profile slurm
exists?
I've solved my issue by installing Snakemake in a Conda environment, and re-installing the profile. I'm not sure if it was the Conda environment or the profile re-install that fixed my issue.