fgvieira / pbs-torque

pbs-torque

This profile configures Snakemake to run on the Torque Scheduler.

Setup

Deploy profile

To deploy this profile, run

mkdir -p ~/.config/snakemake
cd ~/.config/snakemake
cookiecutter https://github.com/Snakemake-Profiles/pbs-torque.git

Then, you can run Snakemake with

snakemake --profile pbs-torque ...

Parameters

The following resources are supported by on a per-rule basis:

node - set the ppn resource request (defaults to the thread declaration).
mem - set the memory resource request (bytes).
mem_mb - set the memory resource request (megabytes).
mem_gb - set the memory resource request (gigabytes).
walltime / time - set the walltime resource (secs).
walltime_min / time_min - set the walltime resource (mins).
walltime_h / time_h - set the walltime resource (hours).