glaunay / ardock Goto Github PK

#ARDock server implementation

git clone https://github.com/glaunay/ardock.git
npm install

Check the config file $scripts/package.json$ for correct path and r/w permissions

##Tests ####1. Basic pdb parsing Test with the default input PDB file (./scripts/test/4MOW.pdb)

$node index.js --conf scripts/package.json --pdb --test  

Specify a valid pdb file

$node index.js --conf scripts/package.json --pdb -f scripts/test/1BRS.pdb

####2. Computing engine The slurm and local implementations require netcat (nc command) to be installed

#####2.1 Local machine (multi-threaded) implementation

$node index.js --conf scripts/package.json --pdb -p 3 --local --test --slurm

Use the --test flag to mimic a docking computation on the pdb file scripts/test/4MOW_D.pdb

#####2.2 Cluster of machines implementation (SLURM only) Perform a 10 probes surface sampling of the 1BRS.pdb A,B dimer

$node index.js --conf ./scripts/package.json --pdb -f ./scripts/test/1BRS.pdb -c A,B --slurm -p 10

####3. Running the HTTP server

#####3.1 Start the HTTP server on test mode $node index.js --conf ./scripts/package.json --test --http

See result at http://ardock.ibcp.fr/test Node server listens on port 3000

#####3.2 HTTP Server with supports for Interactive web-client and REST interfaces

node index.js --conf ./scripts/package.json --http --slurm --rest -p 3

######3.2.1 REST API specifications Using the REST interface to trigger the download of a structure and process it. Results will be displayed as an annotated protein structure file

eg: http://ardock.ibcp.fr/rest?pdbCode=1BRS&chains=A,B

• pdbCode is valid PDB identifier (mandatory)
• chains is a list of chain identifiers separated by coma (optional, by default all valid chains are processed)

######3.2.2 Web-client specifications

IO Duplex connection communication protocol

Usage

Build the client code

$browserify -t browserify-css app.js -o js/bundleTest.js