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 connect analyses in a scripting 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)
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.
If you run the clcserver command with the above parameters, and nothing else, then a list of all commands that can be run on the server will be returned. For example:
clcserver -S server.com -U bob -W secret
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. For example, a command of a form like:
clcserver -S server.com -U bob -W secret -A read_mapping
would return the full list of parameters for the read_mapping function, including the possible values, and descriptions. This information, for each command, is also available in the "Usage for CLC Server name" chapters.
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>
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.
Subsections
- Handling passwords
- Managing SSL certificates
- Data objects, data files and the CLC URL
- Result files and connecting analyses in pipelines
- Executing workflows
- Emptying the recycling bin for a CLC Server File Location