Options

From Array Suite Wiki

In OScript

Used to specify multiple options in a module. Options are usually separated with a "/" and therefore any values containing "/" (e.g. file paths) should be quoted like:

Options /ParallelJobNumber=2 /Mode=Paired /ErrorOnStdErr=True /RunOnDocker=True /ImageName="qdidiscoveryservices/sentieon_omicsoft:202010.03" /OutputFolder="/Users/qc/test";

Warning.png WARNING: The Suite logic will attempt to detect values with "/" and add enclosing quotes to the whole value which can cause nested quoting problems. For example, this /DockerArgs value

Options /RunOnDocker=True /DockerArgs=--volume "/tmp/docker temp":/hostTmp /ImageName="qdidiscoveryservices/sentieon_omicsoft:202010.03" /OutputFolder="/Users/qc/test";

would end up becoming:

Options /RunOnDocker=True /DockerArgs="--volume "/tmp/docker temp":/hostTmp" /ImageName="qdidiscoveryservices/sentieon_omicsoft:202010.03" /OutputFolder="/Users/qc/test";

To avoid this, be sure that anytime a "/" is present in the value, the first and last characters of the value are " e.g. these different variations of /DockerArgs values will be left as-is (no additional quotes will be added by the Suite):

// For the /DockerArgs Option in particular, quoting each argument works well when running on the local OmicSoft Server:
Options /RunOnDocker=True /DockerArgs="--volume=/opt/oshell:/oshell" "--env=bwt_max_mem=15G" /ImageName="qdidiscoveryservices/sentieon_omicsoft:202010.03" /OutputFolder="/Users/qc/test";
// While quoting the entire list of arguments works well when running on cloud:
Options /RunOnDocker=True /UseCloud=True /DockerArgs="--volume=/opt/oshell:/oshell --env=bwt_max_mem=15G" /ImageName="qdidiscoveryservices/sentieon_omicsoft:202010.03" /OutputFolder="/Users/qc/test";


For ExecuteCommand

Options are specified. Each option should be on a new line in the oscript.