AutoDock Gateway for Molecular Docking Simulations in Cloud Systems - Cloud Computing with e-Science Applications - page 228

Desktop grid application Cloud executable

Self-extracting shell script

Vina Application

Gitbox wrapper executable Makeself

packaging

Gitbox wrapper executable

Gitbox script Gitbox script

Vina executable Vina executable

FIGURE 10.9
Multiexecutable desktop grid application bundled into a self-extracting shell script.

representing the supporting files that have to be added to the workflow node
or a single self-extracting archive can be created based on all the executable
files. Simply, this self-extracting archive should be specified as the applica-
tion to run for the workflow node.
In the case of the Vina application, we followed the second approach, with
the help of the makeself UNIX tool [ 10 ]. Figure 10.9 illustrates this multiple
executable file problem and the solution. The executables belonging to the
DG AutoDock Vina application are bundled into a single self-extracting shell
script that can be used as the executable for the Vina node in the Vina work-
flow when configuring the node to run on the cloud.

10.5 AutoDock Gateway
This section explains how to provide user-friendly gateway interface for the
end-user scientists who are not interested even in the workflows. They just
want to use the AutoDock workflows as black box applications and param-
eterize and run them in an efficient and fast way in the connected cloud
systems. In the previous sections, we showed how to use WS-PGRADE/gUSE
to develop and configure the workflows to run in clouds. In this section,
we show a unique feature of our gateway technology. This is the end-user
view of the WS-PGRADE gateway that can be easily created without any
further programming by simply reconfiguring the gateway. In this view, the
end-user scientists cannot see the workflows, only their parameter options,
through which they can specify their required input parameters. Then, the
gateway automatically executes the AutoDock workflows in the connected
clouds in an optimal way.
Once the AutoDock workflows are ready, it is simple to create an end-user
mode portal for them. Only two steps have to be performed: create templates
of the workflows and set the end-user mode as default on the portal.
The template is a special workflow type in WS-PGRADE/gUSE, contain-
ing all the properties of a workflow and restrictions on which properties