Running IMP3

You can run IMP3 by calling Snakemake with the appropriate settings:

snakemake -s /path/to/IMP3/Snakefile --configfile /path/to/config.file.yaml --use-conda --conda-prefix /path/to/IMP3/conda --cores corenumber

Snakefile defines your workflow that you want to execute.

--configfile specifies the config file for your sample. More info you can find here.

--use-conda enables Snakemake to use conda environments defined for your workflow.

--conda-prefix path to your IMP3 conda directory for the IMP3 conda environments.

--cores specifies the number of threads you want to maximally use at the same time in addition to the thread running the main snakemake command (but note extra limitations set in the config file).

All paths can be relative or absolute.

If you’d like to have a report which lists all IMP3 conda environments, rules and running stats, in addition to the visual outputs, run Snakemake with the --report option:

snakemake /path/to/IMP3/Snakefile --configfile config.file.yaml --use-conda --conda-prefix /path/to/IMP3/conda --cores corenumber --report

If you want to use a batch submission system to run IMP3, add the appropriate arguments (more details here):

snakemake /path/to/IMP3/Snakefile --configfile config.file.yaml --use-conda --conda-prefix /path/to/IMP3/conda --cores corenumber --cluster-config /path/to/IMP3/config/cluster.config.yaml --cluster "{cluster.call} {cluster.runtime}{params.runtime} {cluster.mem_per_cpu}{params.mem} {cluster.threads}{threads} {cluster.partition} {cluster.nodes}"