Skip to content
master
Switch branches/tags
Go to file
Code

Latest commit

 

Git stats

Files

Permalink
Failed to load latest commit information.
Type
Name
Latest commit message
Commit time
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

README.md

Arteria-Runfolder

A self contained (Tornado) REST service for managing runfolders.

The service will watch a directory structure containing Illumina runfolders, and try to determine the state it is in by looking for the RTAComplete.txt file which pops up once the sequencing is finished.

Currently supported states are:

NONE    -> No RTAComplete.txt file available
READY   -> Has found and RTAComplete.txt file
STARTED -> Some type of processing is going on of this runfolder
DONE    -> Processing has finished
ERROR   -> Some problem has been detected

All states can be set via posting to the API. E.g:

curl -X POST --data '{"state": "STARTED"}' http://localhost:9999/api/1.0/runfolders/</path/to/my_runfolder>

This means that the client (e.g. a workflow) is responsible for updating the state, and determining how to handle it.

Try it out:

Install using pip:

pip install -r requirements/dev . # possible add -e if you're in development mode.

Open up the config/app.config and specify the root directories that you want to monitor for runfolders. Then run:

runfolder-ws --port 9999 --configroot config/

This will star the runfolder service on port 9999, and the api dock will be available under localhost:9999/api. Try curl-ing to see what you can do with it:

curl localhost:9999/api

Running the tests After install you could run the integration tests to see if everything works as expected: ./runfolder_tests/run_integration_tests.py

This will by default start a local server, run the integration tests on it and then shut the server down.

Alternatively, you can run the same script against a remote server, specifying the URL and the runfolder directory: ./runfolder_tests/run_integration_tests.py http://testarteria1:10800/api/1.0 /data/testartera1/runfolders

Unit tests can be run with nosetests ./runfolder_tests/unit

Install in production One way to install this as a daemon in a production environment can be seen at https://github.com/arteria-project/arteria-provisioning

About

A webservice used to monitor runfolders from Illumina instruments and check what state they are in (e.g. ready to process or not).

Resources

License

Packages

No packages published