This snakemake profile configures atlas to run on cluster systems.
The resources (threads, memory and time) are defined in the atlas config file.
The units are minutes and mb but can be changed. The mapping between resources and cluster are defined in the key_mapping.yaml. For now We have mapping for Slurm, LSF amnd PBS ).
If you need to define queues, the best way is to list all queues available on your cluster in a table queues.tsv with the maximum resource limitations. There is an example in queues.tsv.example. The wrapper then automatically selects the optimal queue for you. Fantastic, isn't it.
Alternatively you can define/overwrite the queue values for all or some rules via the cluster_config.yaml.
Using this file you can also define account and
overwrite any other parameters defined using the config file.
You need cookiecutter to be installed.
conda install cookiecutter
You should know what the default queue/partition you are using.
To deploy this profile,
mkdir -p ~/.config/snakemake
cd ~/.config/snakemake
cookiecutter https://github.com/metagenome-atlas/clusterprofile.git
Then, you can run atlas on a cluster with
atlas run <options> --profile cluster
If a job fails, you will find the "external jobid" in the error message.
You can investigate the job via this ID.
By default the cluster logs are saved in the folder cluster_logs