How to register an application in BOWS. This can be done by a webservice transaction or by filling this form in BOWS services website. In this example, a Submit Job client for running MUSCLE would be automatically compiled and disposed in the website (see the green button in Figure 3). To run the application, the command line would be: java -jar runmuscleSumitJob.jar -sequence_file <myfile> -user <name>. A link for creating the “arrow” program would appear (red button in Figure 3). It downloads a base “arrow” (Arrow_runmuscle.jar), a shell script (Arrow_runmuscle.sh) to complement the base “arrow” by informing the application execution command line in it, and a shell script to edit cron scheduler to execute the “arrow”.