Usage

## Command-line parameters

List of current parameters for command-line usage and their explanation:

Usage: uropa [options]

Available options:

-h, --help                              print this help message and further details on the configuration file
-i confing.json, --input confing.json   filename of configuration file [mandatory]
-p prefix, --prefix     prefix          prefix for result files, can include subdirectories [basename of config]
-r, --reformat                          create an additional compact and line-reduced table as result file
-s, --summary                           additional visualisation of results in graphical format will be created
-t n, --threads n                       multiprocessed run: n = number of threads to run annotation process
-add-comments                           show comment lines in output files explaining the columns
-l uropa.log, --log     uropa.log       log file name for messages and warnings
-d, --debug                             print verbose messages (for debugging purposes)
-v, --version                           print the version and exit

Note

The -p parameter can either contain the prefix of the result files, like -p abc gives abc_allhits.txt in the working directory, or the result directory and prefix, like -p xy/abc which stores the result files in directory xy. If the directory xy is not existing, it will be created.

## Docker container usage

sudo docker run --rm -v <path-to-input-files-on-HOST>:<path-to-container-mnt> UROPA:LATEST uropa <UROPA-Paramters> -p <path-to-container-mnt>/'your-file-prefix'

Note

-v parameter mounts a HOST folder into your docker CONTAINER. This folder should contain the input files for UROPA and also the result files will be stored here. No files will be stored in the container!! --rm removes/closes the container after the run Make sure to use the uropa -p option specifying the output directory and prefix, otherwise results are lost in the container environment!