# VirtualFlow Commands ## Overview of Commands VirtualFlow provides the following commands for users: * `vf_prepare_folders.sh` * `vf_start_jobline.sh` * `vf_continue_jobline.sh` * `vf_continue_all.sh` * `vf_report.sh` * `vf_redistribute_collections_single.sh` * `vf_redistribute_collections_multiple.sh` ## Location All VirtualFlow commands are all stored in the `tools` folder. These commands start with the prefix `"vf_"`. The `tools` folder is also the primary working directory for any user-command available in VirtualFlow, meaning that all VirtualFlow 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. --- # Agent Instructions: Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter: ``` GET https://docs.virtual-flow.org/documentation-vf1/using-virtualflow/overview-of-commands.md?ask= ``` The question should be specific, self-contained, and written in natural language. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.