anjanasenanayake / f5n_server Goto Github PK

This is a job server to distribute sequencing tasks among portable devices that run f5n

1. Clone the repository**

git clone https://github.com/AnjanaSenanayake/f5n_server.git

2. Inside the cloned directory, compile source code**

mvn install

3. Deploy in a jetty server(Feel free to use any server, jetty dependencies are already added in pom)**

mvn jetty:run

4. Open localhost in any web browser.**

The source code for the Mobile Application can be found here

1. Download a dataset
2. Pair each reads.fastq(a) and the corresponding (multi)fast5 files. refer scripts.
3. Compress each pair as a .zip file. (you should now have a folder with many number of .zip files)
4. Run f5n-server
5. Configure the folder path to the folder containing the .zip files.
6. Configure a pipeline
7. Create jobs
8. Connect to f5n-server with mobile phones using the local IP address.

Since client-server communication happens only when a job is requested or to get updates of a job, server side is not multi-threaded. Rest of the client requests have to wait while the first client is served. Once a client is served(ex:a job is assigned) the socket is closed. Average service time is minimal thus, we assume mutli-threaded server will not enhance the performance. Also the fact that not all the clients try to connect to the server at the same time supports this. Moreover, there is a considerable time gap between intermediate minIT ouputs. Hence, a client may have to wait until a new job get listed.

minIT is changing their output file format continuously. Hence we advice the user to alter the code to cater for different scenarios.

• stop server & reconfiguration pipeline components
• data set update listner
• pipeline configuration form validations
• user messages/warnings/errors to frontend