Medical Bioinformatics and e-Bioscience

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General Executor

Motivation

It would be helpful for some researchers to send an executable with the input data to the grid, and specify the command needed to be performed on the data.

Goal

To make the grid more accessible to biomedical researchers, by providing a workflow that allows to run arbitrary software on the grid.

Usage

Preparing the executable and the data

The common practice to prepare your executable and data to be used with the GE is like the following:

1. put the executable(s) with all needed libraries, options file, etc in one "binary.tar". Include here also a shell script that will call your executable(s) in the right way in the called command (e.g. with parameters, option file, more than one executable with special order…)
2. put your data in the needed hierarchy of directories in the “data.tar”

An example can be found in lfn://lfc.grid.sara.nl:5010/grid/vlemed/yassene/generalexecutor/test.

Calling the the GE

The GE can be used by starting the vbrowser and calling to the following file using the Moteur2 viewer: lfn://lfc.grid.sara.nl:5010/grid/vlemed/yassene/generalexecutor/GEv1.gwendia

The GE needs three inputs (see image):

1. the data,
2. the binary, and
3. the command.

The “data” and the “binary” should be normal tared (.tar, no .tgz); but this can be also modified easily if it is needed. The “command” is the command line of the executable with no parameter. In case that parameters are needed, one can put everything in a shell file and call that shell file as one command without parameters in the gwendia workflow.