D6.1:Prototype Implementation

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Installation

   export http_proxy=http://user:password@host:port
   export https_proxy=https://user:password@host:port
   vagrant plugin install vagrant-proxyconf


  • Optionally, edit the west-life-wp6/vagrant/Vagrantfile to match the http-proxy and https-proxy to your environment:
   vagrant/Vagrantfile
   ...
   config.proxy.http     = "http://yourproxy:8080"
   config.proxy.https    = "http://yourproxy:8080"
   config.proxy.no_proxy = "localhost,127.0.0.1"
  • Open command-line (e.g. cmd, cygwin or terminal)
   cd west-life-wp6
   cd vagrant
   vagrant up

This will start to download and install appropriate packages - depending on network speed it will take several to several tens of minutes - downloading 200 MB of data.

Usage

The new virtual machine can be access by SSH (by default the 2222 port is forwarded to VM)

   vagrant ssh

Or via web browser (port 8080 is forwarded to VM)

   http://localhost:8080/

Current state of prototype implementation

After self deployment and installation the virtual machine provides 3 basic services:

Web application at http://localhost:8080

Configure b2drop connection

Wp6config.png

Processing application

artefacts can be dragged and dropped into appropriate workflows

Wp6processing.PNG

PDB repository

integration with PDB.ORG, other PDB database might be added

Wp6pdb.PNG

List of scratch data

Wp6list.PNG

WEBGL viewer of PDB files

Wp6ngl.PNG

full NGL browser

Wp6ngl2.PNG

WebDAV to shared data

at http://localhost:8080/webdav/

Wp6webdav.PNG

Other tools

  • Preinstalled and preconfigured CCP4 suite to allow further data refining, processing, analysis and automatic execution of XIA2 workflow on new data in webdav/mydata/xia folder

Notes

The webapp is currently based on PHP scripts for DOKUWIKI and it's plugins on Apache web server. Further development will probably not continue with PHP server side processing and will follow rather RESTful web services (Java, Python, ...) and HTML and Javascript (AJAX) on client.