Environment Variables

There are several environment variables that affect the way Toil runs.

TOIL_WORKDIR An absolute path to a directory where Toil will write its temporary files. This directory must exist on each worker node and may be set to a different value on each worker. The --workDir command line option overrides this. On Mesos nodes, TOIL_WORKDIR generally defaults to the Mesos sandbox, except on CGCloud-provisioned nodes where it defaults to /var/lib/mesos. In all other cases, the system’s standard temporary directory is used.
TOIL_APPLIANCE_SELF The fully qualified reference for the Toil Appliance you wish to use, in the form REPO/IMAGE:TAG. quay.io/ucsc_cgl/toil:3.6.0 and cket/toil:3.5.0 are both examples of valid options. Note that since Docker defaults to Dockerhub repos, only quay.io repos need to specify their registry.
TOIL_DOCKER_REGISTRY The URL of the registry of the Toil Appliance image you wish to use. Docker will use Dockerhub by default, but the quay.io registry is also very popular and easily specifiable by settting this option to quay.io.
TOIL_DOCKER_NAME The name of the Toil Appliance image you wish to use. Generally this is simply toil but this option is provided to override this, since the image can be built with arbitrary names.
TOIL_AWS_ZONE The EC2 zone to provision nodes in if using Toil’s provisioner.
TOIL_AWS_AMI ID of the AMI to use in node provisioning. If in doubt, don’t set this variable.
TOIL_AWS_NODE_DEBUG Determines whether to preserve nodes that have failed health checks. If set to True, nodes that fail EC2 health checks won’t immediately be terminated so they can be examined and the cause of failure determined. If any EC2 nodes are left behind in this manner, the security group will also be left behind by necessity as it cannot be deleted until all associated nodes have been terminated.
TOIL_SLURM_ARGS Arguments for sbatch for the slurm batch system. Do not pass CPU or memory specifications here. Instead, define resource requirements for the job. There is no default value for this variable.
TOIL_GRIDENGINE_ARGS Arguments for qsub for the gridengine batch system. Do not pass CPU or memory specifications here. Instead, define resource requirements for the job. There is no default value for this variable.
TOIL_GRIDENGINE_PE Parallel environment arguments for qsub and for the gridengine batch system. There is no default value for this variable.
TOIL_TORQUE_ARGS Arguments for qsub for the Torque batch system. Do not pass CPU or memory specifications here. Instead, define extra parameters for the job such as queue. Example: -q medium Use TOIL_TORQUE_REQS to pass extra values for the -l resource requirements parameter. There is no default value for this variable.
TOIL_TORQUE_REQS Arguments for the resource requirements for Torque batch system. Do not pass CPU or memory specifications here. Instead, define extra resource requirements as a string that goes after the -l argument to qsub. Example: walltime=2:00:00,file=50gb There is no default value for this variable.
TOIL_LSF_ARGS Additional arguments for the LSF’s bsub command. Instead, define extra parameters for the job such as queue. Example: -q medium There is no default value for this variable.