# GS Amplicon Variant Analyzer CLI script used to populate new projects

#

# This script adds the "Standard" 454 MIDs to the project and

# then runs the user-specific initialization script found in the user's

# home directory, if any.

#

# Sites may want to edit this file to further customize the initialization

# of new AVA projects.  To completely disable the actions of this file,

# comment out, or delete, all its lines:  do not delete the file itself, 

# however, or else a warning message about a missing file will be displayed 

# each time a new project is created from the gsAmplicon application GUI.

# Step 1: Populate with the "Standard" 454 MIDs

#         (To prevent this, comment out or delete the following line:)

utility execute create454StandardMIDs.ava

# Step 2: Run whatever "new project" scripts are in the

#         user's home directory.

#         (Note, due to the use of -onMissingScript with the value 'ignore',

#          it is not an error if the user has no such script)

utility execute -onMissingScript ignore %homeDir/.gsAmplicon_newProjectInit.ava

Fourteen MIDs were carefully selected four use with Amplicon libraries, in the 454 Sequencing System (section 1.3.2.6). As part of the default initialization process, these MIDs are automatically loaded into the Project as a convenience and as a means of reducing data entry error. The command ‘utility execute create454StandardMIDs.ava’ runs a default script called ‘create454StandardMIDs.ava’ that is located in the same directory as the default initialization script (‘installDir/apps/amplicons/config/lib’). The script creates Amplicon MIDs Mid1-Mid14 in the Project.

Since the default initialization script is part of the main software installation, the average user probably will not have permissions to edit the script. To enable users to customize the automated project initialization, the default script calls through to a script in the user’s home directory called ‘.gsAmplicon_newProjectInit.ava’ by using the command ‘utility execute ‑onMissingScript ignore %homeDir/.gsAmplicon _newProjectInit.ava’. Thus, users can create a script called ‘.gsAmplicon_newProjectInit.ava’ in their home directory, and fill it with CLI-commands to add extra functions to the initialization process. (Note that the file name intentionally begins with a ‘dot’, which makes the file invisible to standard listings of the user’s home directory.) The customized user script is entirely optional, however; no errors or warnings will be issued if the user does not create one.

The name of the user-customized script is dictated by the command issued in the default initialization script. If the administrator changes the name of the called script by editing the default initialization script e.g. so that the Step 2 command is ‘utility execute ‑onMissingScript ignore %homeDir/.gsAmplicon _user_customization.ava’, then the corresponding user-customized script would have to be named ‘.gsAmplicon_user_customization.ava’.