python3 scout_knife.py NameOfTaxa
Though it is meant to run in the background so it can be smart running it in detached:
python3 scout_knife.py NameOfTaxa &
And then It might be smart to the output to a file so:
python3 scout_knife.py NameOfTaxa &> scout_knife_log.txt
To use the config you have to create a .config file in the working directory. Below desibes the different parameters you can add to the config file. There is also an example config file in this repo called .config_example
Default Value: None, Type: str
Example in .config: webhook_url=https://discord.com/api/webhooks/{webhook_id}/{token}
The config is very basic and just change some of it parameters, the only one that does not have a default value is webhook_url so that one should be set if you want to support logging to a webhook.
The request is a POST request with this header:
{
"method": "POST",
"Content-Type": "application/json"
}and with this as json body if the link had discord in it:
{
"content": message
}this the link contains slack
{
"text": message
}otherwise it just send the payload as a string (message) in the request.post() method's data parameter
where message is a string from the script that it want to report typically errors or starting and ending of a batch
At the moment it is only tested with the discord webhook api.
Default value: 10, Type: int
Example in .config: max_size=10
This is how many sub_process to run concurrently.
Default value: 1, Type: int
Example in .config: sub_process=1
This is the starting point of the id of the sub process
Default value: 100, Type: int
Example in .config: max_sub_process=100
So it will create a process with id starting from sub_process and it will run max_size at the time. When the process id hits max_size it will stop creating more process and eventually exit, when all its sub_process has completed.
Default value: 1800 (30 minutes), Type: int
Example in .config: sleep_time=1800
How long in seconds it will sleep in between checks to see if the processes are still running and spawn new once.
Default value: 10, Type: int
Example in .config: start_timer=10
How long in seconds it will wait before running sbatch
kill -12 <pid> Will kill the process and all the jobs that the script created (No other jobs should be cancelled)
kill -10 <pid> Will eventually killed the process, once it sees that all current jobs are completed (this means it will still be running for a while and reporting, but it will no longer start any new once, and will eventually finish)
kill -15 <pid>, kill -2 <pid> (same as ctrl+c) will shut it down immediately, however all jobs running will continue to run