Here are many available commands for use in the pipeline:

Note that example is the name of a project.

Commands included as part of MetaProD:

generate_fasta

Function: Generates the initial profile fasta for a project. This should be done for every project before it is run.

Usage: ./generate_fasta project_name

Example: ./generate_fasta example

update_queue

Function: Updates the queue for project. It first checks to ensure all files that are in the "raw" folder for the project have been added to the queue. It then checks to see if all queued files have finished the profile step. If they have, it updates the NSAF values and generates the FASTA for the full-proteome search. It finally checks to see if all files have finished the full-proteome step. If they have, it updates the NSAF values for the project.

Usage: ./update_queue project_name

Example: ./update_queue example

check_status

Function: This checks the status for all the files in a particular project and prints the result.

Usage: ./check_status project_name

Example: ./check_status example

run_queue

Function: This runs the file queue for a project. It has an optional component to specify the job so that it will only run files for that job.

Usage: ./run_queue project_name or ./run_queue project_name job

Example: ./run_queue example or ./run_queue example 0

analyze_results

Function: Generates the differentially expressed proteins for a project that is configured to be multiplexed and set to run DEqMS. If this command is run, no differentially expressed proteins will be generated nor included in the results webpage. Non-multiplexed projects are currently not supported.

Usage: ./analyze_results project_name

Example: ./analyze_results example

generate_secret.py

** Function:** Generates a new secret key for Django and prints it out. This is useful to change the default secret key MetaProD comes with.

Usage: python3 generate_secret.py

Commands included as part of Django:

Django includes many commands. A full list of commands can be obtained by running: python3 manage.py. See the Django documentation (python3 manage.py help subcommand for information about most of these commands but we have included information about some more commonly-used ones.

python3 manage.py createsuperuser

Function: Creates the initial super user for the website. This needs to be done to create the initial login for the admin website. Further users can be created inside the admin website.

Usage: python3 manage.py createsuperuser

python3 manage.py dbshell

Function: Allows one to access an SQL shell to run SQL queries to manipulate the projects and results databases. Warning: This can have unexpected results so it should be used carefully.

Usage: python3 manage.py dbshell

python3 manage.py shell

Function: Allows one to access a Python shell to run Python-based commands. Warning: This can have expected results so it should be used carefully.

python3 manage.py runserver

Function: This runs a local webserver, primarily for testing or local access. Note that the port assigned for the webserver should be listed in the metaprod/settings.py file under "ALLOWED_HOSTS" (e.g. ALLOWED_HOSTS = ["10.0.0.10"]).

Usage: python3 manage.py runserver ip_address:port

Example: python3 manage.py runserver 10.0.0.10:8080

python3 manage.py flush

Function: Wipes the database. This will wipe all entries in the queue, settings, results, etc. so it should be used very carefully.

Example: python3 manage.py flush