Failed to run without `mamba`

[dr-joe-wirth]

I installed seabreeze as described using conda 24.5.0. It failed to run:

(base) dr-joe-wirth@<REDACTED>:~/seabreeze_review/seabreeze-1.3.0$ conda --version
conda 24.5.0
(base) dr-joe-wirth@<REDACTED>:~/seabreeze_review/seabreeze-1.3.0$ conda activate seabreeze
(seabreeze) dr-joe-wirth@<REDACTED>:~/seabreeze_review/seabreeze-1.3.0$ ls ./
JOSS  LICENSE  README.md  Snakefile  bin  data  documentation  environment.yml  example  pytest.ini  test
(seabreeze) dr-joe-wirth@<REDACTED>:~/seabreeze_review/seabreeze-1.3.0$ ls ./data
02_genomes  data.csv  ori_dif_sequences.csv
(seabreeze) dr-joe-wirth@<REDACTED>:~/seabreeze_review/seabreeze-1.3.0$ snakemake --use-conda --cores 4 analyse_genome_sizes
Building DAG of jobs...
CreateCondaEnvironmentException:
The 'mamba' command is not available in the shell /usr/bin/bash that will be used by Snakemake. You have to ensure that it is in your PATH, e.g., first activating the conda base environment with `conda activate base`.The mamba package manager (https://github.com/mamba-org/mamba) is a fast and robust conda replacement. It is the recommended way of using Snakemake's conda integration. It can be installed with `conda install -n base -c conda-forge mamba`. If you still prefer to use conda, you can enforce that by setting `--conda-frontend conda`.

This was fixed by appending --conda-front-end conda to my snakemake command. I'd suggest including this information in your documentation.

This is part of the review at openjournals/joss-reviews#8065

[ira-zibbu]

Hi @dr-joe-wirth

Thanks for notifying me of this issue. I have updated this information in the documentation in the usage page.