SeqWare › Sanity Check

Seqware Sanity Check is a tool developed in order to see if the seqware environment is set up correctly in a given system. It runs preliminary checks and will return an exit code of 0 if all the checks have passed. The tool also contains different parameters in order to specify certain tests to be included or not.

Requirements

In order to run the Sanity Check tool, you must have the following available to you:

SeqWare Distribution JAR (1.0.14 or higher)
Seqware Sanity Check JAR (1.0.14 or higher)
SeqWare settings file set up to contact the SeqWare Web service (contact your local SeqWare admin to get the path)

Command line parameters

You can annotate the following attributes:

Command-line option	Description
–master, -m	Master mode. Use this if you are running on a master node. Will do more admin testing if included.
–tutorial, -t	Runs through the seqware tutorial as well.
–help, -h	Displays this list of parameters.

Examples

Running the sanity tool on a user node.

java -jar seqware-sanity-check/target/seqware-sanity-check-1.0.14-SNAPSHOT-jar-with-dependencies.jar

Running the tool on a master node.

java -jar seqware-sanity-check/target/seqware-sanity-check-1.0.14-SNAPSHOT-jar-with-dependencies.jar --master

Running the tutorial as well

java -jar seqware-sanity-check/target/seqware-sanity-check-1.0.14-SNAPSHOT-jar-with-dependencies.jar --master --tutorial

Help

java -jar seqware-sanity-check/target/seqware-sanity-check-1.0.14-SNAPSHOT-jar-with-dependencies.jar --help

Results

Once all the tests are completed, an exit code will be returned. If the exit code is non-zero, then one of the checks specified has failed. The stacktrace will also be displayed if an error occurs while running the checks.