Command line tools


ProCope provides a collection of command line tools which provide fast access to many methods and functions in a way suitable for automated computations and batch jobs. In this part of the documentation you find general information on how to access these tools as well as descriptions and example calls for each single tool.

Note: All tools detect GZIPed input files and automatically decompress them.

Calling from the command line

All tools are called using a single script file which can be found in the root directory of the package:
The first argument you pass to the script is the name of the command line tool you want to use. Specifiy no parameters to get a list of available tool names (or consult this documentation). Each command line tool itself will print usage information when called without any further parameters.

Note: All examples in this documentation use the cmdline.sh script for bash shells. Windows users simply replace this command with cmdline.bat.

Example:
cmdline.sh colocalization - starts the colocalization tool and shows usage information as no further parameters are passed

Memory

By default 256MB of memory will be available for the Java VM when using a command line tool. If you want to change this amount, specificy -Xmx000m as the first argument where 000 is the amount of megabytes which will be available. (Note: the -Xmx parameter is directly passed to the Java virtual machine, syntax errors will cause error messages of the Java interpreter).

Example:
cmdline.sh -Xmx1024m generatescores ... - starts the scores generator with 1GB of available memory

Return codes

All command line tools return

Name mapping

All tools support the argument -namemap. See also: Name mapping

Tools

The following command line tools are provided with this package:



ProCope documentation