VirtualFlow 2.0 Commands

Overview of Commands

VirtualFlow 2.0 provides the following commands for users:

• vflp_prepare_folders.py

• vflp_prepare_workunits.py

• vflp_run.py

• vflp_submit_jobs.py

• vfvs_prepare_folders.py

• vfvs_prepare_workunits.py

• vfvs_submit_jobs.py

• vfvs_verify_collections.py

Location

All VirtualFlow 2.0 commands are all stored in the tools folder. These commands start with the prefix "vflp_" for the VFLP 2.0 module and the prefix "vfvs_" for the VFVS 2.0 module. The tools folder is also the primary working directory for any user-command available in VirtualFlow 2.0, meaning that all VirtualFlow 2.0 commands have to be executed while being in this folder.

Executing Commands

In order to be able to execute the commands in the tools folder, they need to either prefixed with the ./ to be found by BASH, or their locations needs to be in the PATH variable. We do not recommend to put the absolute path of the tools folder into the PATH variable, because then these command are globally available. But different versions and different modules of VirtualFlow can be run in parallel, and they might use different versions of these commands. Therefore, it is best to use the local versions which are stored in the tools folder belonging to each workflow. However, one can put the current working directory into the PATH variable:

export PATH="$PATH:."

The current working directory should always be added at the right-most position of the PATH variable due to security and safety reasons (otherwise, commands in the current working directory can override important system commands). To permanently include the current working directory in the PATH variable, one can put the above line into the file ~/.bashrc file.

Help

Each command has a -h (help) option to display basic usage information.