Creating a New Project

3. GS Amplicon Variant Analyzer Command Line Interface : 3.5 Creating and Computing a Project with the AVA-CLI : 3.5.2 Creating a New Project

3.5.2

Creating a New Project

The first step in creating a Project is setting up the Project directory structure that will store the Project configuration, data, and results. This is done using the “create project” command (see section 3.4.4.2 for the usage statement). Here is an example Project creation command:

create project /data/ampProjects/EGFR_CLI \

    -name EGFR_CLI \

    -annotation "CLI Example Project Creation Test"

Note the backslash character (“\”) used to indicate line continuation. This allows you to control the format of the command over multiple lines, to improve the readability of long commands. This command could also have been presented as one continuous line without the backslashes. Note also the multi-word annotation included within double-quotes. Double-quotes allow spaces and unusual characters to be included in argument values. See section 3.3.2.2 for other specifics on how commands are formatted and parsed. Finally, note that creation of the directory structure for the Project occurs at the time that the “create project” command is executed and is the one aspect of Project definition that will not be reverted if you choose not to save before exiting the CLI.

The “create project” command can be used only once for any given Project. To continue the set up or other work on a Project that has been previously created, use the “open” command (see section 3.4.9 for the usage statement). To open an existing Project, you simply type the Project path after the open command, e.g.:

open /data/ampProjects/EGFR_CLI

Note that this is the actual path to the Project and not the name of the Project. The last part of the Project path and the Project name often coincide because the default name for a Project can be based on the Project directory (see section 2.2.2 for an example of this), but the Project path and the Project name can also diverge (such as if the Project is moved to a new location, perhaps for reasons related to disk space, in which case the Project name would stay the same but the Project path would change). If you try to open a Project that is already open by someone else and you are in interactive mode, a warning will appear and will give you the option to preempt control or to continue with read-only access. If you are using an open command in a script in non-interactive mode, the open command will fail and throw an error that will halt your script (unless onErrors is set to continue).

If you want to intentionally open a Project in read-only mode, you can use the “‑control readonly” parameter as part of your open statement. You can also explicitly set the control to “‑control preempt” to seize control of the Project you are opening even if someone else is working with it.