HexTask

Hextask is an instance of taskobject (Git repo, NPM package), used to process a simple Hex job (Hex website).

Installation

In your project repository :

npm install hextask

Usage

You can either make a test in your proper JS file or use the test file we provide.

Your proper test

In your JS script, import the test file :

var hexTestModule = require('./node_modules/hextask/test/test');

Then you have to start and set up a JM (= Job Manager, more info in the More section). We provide a method that takes care of that :

hexTestModule.JMsetup();

JMsetup returns an object instance of EventEmitter. It emits "ready" when the JM is ready to receive jobs, and provide the JM object. Then, you can run the hexTest method :

hexTestModule.JMsetup().on('ready', function (JMobject) {
    hexTestModule.hexTest(pdbFile, management, probeContent, ncpu);
});

• pdbFile is the absolute path to your PDB file.
• probeContent is the content of the PDB file of your probe.
• ncpu is the number of CPUs on which you want to run Hex. WARNING : for now, only 16 is available !
• management is a literal like :

let management = {
    'jobManager' : JMobject // provided by the JMsetup method
}

The hexTest method :

1. creates a stream (Readable) containing a JSON with your pdbFile content,
2. instantiates a hextask (more info on the Hex website),
3. pipes the stream on the hextask, also piped on process.stdout, so you can watch the results in your console.

The test file

The previous test is already implemented in the ./node_modules/hextask/test/ directory. To use it :

node ./node_modules/hextask/test.js

This script needs some command line options. You can use option -u to display the documentation.

Loading library

In your JavaScript module :

var hexModule = require('hextask');

Creating an instance of hextask - not updated !!!!

In your JavaScript module :

var h = new hexModule.Hex (management);

Note that you need a job manager to use hextask, like nslurm (GitHub repo, NPM package) adapted to SLURM manager.

Using in a pipeline - not updated !!!!

In your JavaScript module :

readableStream
    .pipe(h)
    .pipe(writableStream);

Setting the hextask - not updated !!!!

You can modify the parameters in the ./data/settings.json file :

{
    "coreScript": "./data/run_hex.sh",
    "automaticClosure": false,
    "settings": {} // proper hex parameters
}

Proper hextask parameters must be defined in the "settings" part of the JSON.

More

Job Manager

Coming soon...
A Job Manager (JM) is necessary to run a Task. In our case, we use the nslurm package (GitHub repo, NPM package), adapted for SLURM.