Options

From Array Suite Wiki

Jump to: navigation, search

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 variatiosn of /DockerArgs values will be left as-is (no additional quotes will be added by the Suite): 

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

The first of these variations is likely the safest - you may need to test if the last 2 variations would be interpreted by the docker run command as expected.


For ExecuteCommand

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