Basic usage

Once installed, there will be four programs present in the installation folder:

clcserver - the key program. It is used to run all the commands that communicate with the server.
clcresultparser - used to parse data locations from particular text files generated during clcserver runs. This command is most useful when connecting analyses in a scripted pipeline.
clcserverkeystore - a helper tool for enabling passwords to be handled securely (see Handling passwords).
clcserversslstore - a helper tool for managing SSL certificates (see Managing SSL certificates)

Getting help

Run the clcserver command with no arguments or with an incomplete set of arguments to see information about what can be run on the server. Below is a list of command forms, and the type of information produced using them.

clcserver Running just this command with no arguments returns general information and options.
clcserver -S <server> -U <username> -W <password or token> A command of this form returns a list of all the commands that can be run on that server.
clcserver -S <server> -U <username> -W <password or token> -A <task name> A command of this form returns all the options available when submitting that task to the server.

The clcserver command - details

The clcserver program requires the following four flags, which provide information about the connection to the server:

-S <hostname or IP address of the server>
-P <port the server runs on>: When omitted, port 7777 is used, which is the default for server installations.
-U <user name>: The username used to log into the server.
-W <password or token>: See Handling passwords for how to avoid entering passwords in clear text.

The commands to be run on the server are supplied with the flag:

-A <command to be executed on server>

If you supply the -A flag with a program name, but do not provide the required flags for that program, then a listing of the flags for that program will be returned.

An optional flag when working on the command line, but important when working with scripts, is:

-O <filename>: The name of a file to be created to hold a summary of steps carried out on the server and data locations of the results generated. The data locations are of a form that can be used by downstream CLC commands. See Result files and connecting analyses in pipelines for information about parsing this file. By default, this file is placed in your working directory."

For those working with the CLC Grid Integration Tool, you can run import and algorithm commands through your grid nodes by adding the following flag to your clcserver command:

-G <grid preset name>

Options available for managing and querying jobs and results include:

-Y: Execute the command asynchronously. The returned process ID can be used to query for status and results by using the -I and -R flags, respectively.
-I <process IDs>: Return information about the listed processes. If a list of process IDs is not provided, information about all processes submitted by the current user are returned.
-R <process IDs>: Returns the results of the finished processes. Results for a given process can only be retrieved once using this option. To cancel a specific process use
-R <process ID> -R cancel. To cancel all processes owned by current user, use
-R cancel-all. Using that option as an administrative user will cancel all processes.

Other optional flags available for the clcserver command are:

-C <integer>: Specify the column width of the help output.
-D <boolean>: Enables debug mode when set to true, providing more elaborate output and error messages.
-H: Display general help instructions.
-V: Display the version number of CLC Server Command Line Tools.

Hint: When launching multiple tasks via a script, putting sleep 10 between the commands can help keep the memory needed for the waiting command to a minimum. It can also be worth checking that the number of user processes allowed is sufficient (ulimit setting).

Subsections

Browse the manual

Basic usage

Getting help

The clcserver command - details