QIAGEN Bioinformatics Manuals

Using CLC Server Command Line Tools to launch external applications

The CLC Server Command Line Tools can be used to launch CLC tools, workflows and external applications, directly or within a workflow context, on a CLC Server. General information about using the CLC Server Command Line Tools can be found in the manual for that software: https://digitalinsights.qiagen.com/technical-support/manuals/.

When launching an external application, the CLC Server execution context will be used unless another execution environment is specified. For example, by adding the -G option, a grid preset can be specified.

Running a CLC Server Command Line Tools command with missing or invalid parameters results in messages about the problem being returned. For example, trying to invoke the copy external application described earlier in this chapter with no arguments yields the output below. The final line makes clear the problem: the -d and -in parameters need to be specified in the command for the job to be executed.

clcserver -S <HOSTNAME> -U <USER> -W <PASSWORD> -A copy
Message: Trying to log on to server
Message: Login successful
The following options are available through the command line and the types are as follows:
Type                                     Valid input
----                                     -----------
<Integer>                                A decimal number in the range
[-2147483648;2147483647]
Example: 42
<Boolean>                                The string true or false
Example: true
<String>                                 Any valid string. It is recommended
to enclose all strings in '' to
avoid issues with the shell
misinterpreting spaces or double
quotes
Example: 'text="My text"'
<ClcFileUrl>                             A valid path to a file on the server
or in the local file system
Example: clc://serverfile/tmp/export
<ClcObjectUrl>                           A valid path to a Clc object on the
server or locally
Example: clc://server/pstore1/Variant1
Option                                   Description
------                                   -----------
-A <Command>                             Command currently set to 'copy'
-C <Integer>                             Specify column width of help output.
-D <Boolean>                             Enable debug mode (default: false)
-G <Grid preset names>                   Specify to execute on grid.
-H                                       Display general help.
-O <File>                                Output file.
-P <Integer>                             Server port number. (default: 7777)
-Q <Boolean>                             Quiet mode. No progress output.
(default: false)
-S <String>                              Server hostname or IP-address of the
CLC Server.
-U <String>                              Valid username for logging on to the
CLC Server
-V                                       Display version.
-W <String>                              Clear text password or domain
specific password token.
-d, --destination <ClcServerObjectUrl>   Destination for import from External
Application
--in <ClcServerObjectUrl>                Model object(s) to be exported to
FASTA (.fa/.fsa/.fasta)
Error: Missing required options: d, in

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Using CLC Server Command Line Tools to launch external applications