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}"