Toil 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. |