snakemake version problem?

[flowers9]

I just did a new install of CLAW (and required other packages), and I'm getting an error trying to run the example:

#snakemake --profile profiles/slurm --use-conda --keep-going

snakemake: error: unrecognized arguments: --cluster-status=profiles/slurm/status --cluster-config=cluster-configs/slurm.yaml

The snakemake version is 8.5.4 (which is current), and I can't find any reference to those options in the current docs (or the snakemake code). When I looked through the snakemake change logs (https://snakemake.readthedocs.io/en/stable/project_info/history.html), I can find references to them in versions 3.7.0 and 4.1.0.

Is there a particular version (or range of versions) of snakemake that's required for CLAW? Or is my problem something else enitrely?

The only changes I made to the install was adding a default value to cluster.account and adding a cluster.licenses field (required for the slurm cluster I use).

[flowers9]

Yep, looks like snakemake 7.32.4 is the last version that supports CLAW. They broke a lot of stuff in the jump to 8.0.0. Maybe mention it somewhere?

[dreyes17]

Hello,

As far as I have been able to verify, it only works with version 7.30.1, not with 7.32.4.

This is the Dockerfile I have been able to create for it to work correctly. The only prerequisite is to download the CLAW code, rename it from CLAW-main to CLAW, and compress it into a .tar.xz file. This file should be in the same folder as the Dockerfile.

FROM snakemake/snakemake:v7.30.1

WORKDIR /app

COPY CLAW.tar.xz /app/

RUN tar -xf CLAW.tar.xz

WORKDIR /app/CLAW

RUN conda config --set allow_conda_downgrades true

RUN conda config --set auto_update_conda false

RUN conda config --add channels conda-forge

RUN conda config --add channels bioconda

RUN conda create --name snakemake

RUN conda init bash

RUN ["/bin/bash", "-c", "source ~/.bashrc"]

RUN ["/bin/bash", "-c", "conda install mamba -n base -c conda-forge"]

RUN ["/bin/bash", "-c", "mamba install snakemake==7.30.1"]

RUN ["/bin/bash", "-c", "mamba install biopython"]

RUN ["/bin/bash", "-c", "snakemake -j 1 --conda-create-envs-only --use-conda"]

CMD ["tail", "-f", "/dev/null"]