MATLAB APPLICATION DEPLOYMENT - WEB EXAMPLE GUIDE Manuel d'utilisateur

GenePattern Programmer’s Guide

Compiling Your MATLAB Code If you do not plan to use the compiled M-code approach, skip this section and continue with Distributing Your MATLAB Code.

To check that MATLAB is on your path: 1. Open a DOS window. 2. Type matlab and press Enter. If the MATLAB application starts, MATLAB is on your path.

On Windows, to run the MCRInstaller: 1. Copy <matlabroot>\toolbox\compiler\deploy\win32\MRCInstaller.exe to the server machine. 2. Run MCRInstal

The chmod line sets the executable permission on the executable file; by default, the GenePattern server does not set this permission for uploaded fil

Writing the M-file The first step is writing the MATLAB M-file that you want to share. For this example, write a simple application that takes a filen

2. Copy the zip file to your GenePattern server (if it is a different machine) and install it into a directory. For example, add a directory, matlab,

▪ <fname> for the output file name ▪ <txt> for the text to write to the file ● Include the following support files: ▪ mllaunch.bat ▪ w

GenePattern Java Library The GenePattern Java library allows you to invoke a GenePattern task as if it were a local Java method running on your client

new Parameter[] { new Parameter("filename", preprocess.getURL(0).toString()) }); The last statements in the application download the pre

2. Under Programming Libraries in the right column, click the zip link for the MATLAB library. 3. Download the zip file and unzip it into your MATLA

Software Copyright The Broad Institute SOFTWARE COPYRIGHT NOTICE AGREEMENT This software and its documentation are copyright 2006 by the

Alternatively, to get the parameters with their default values filled in, use the getMethodParameters function of the GenePatternServer object. This r

● R Data Import/Export (PDF, approx. 35 pages, 270kB) describes the import and export facilities available either in R itself or via packages which ar

When the task completes, it returns an R list of filenames that are the output from the task. In this example, transpose.out now has a list of filenam

Table of Contents Introduction ...

Introduction This guide assumes that you are a programmer and familiar with GenePattern. If you are new to GenePattern, work through the GenePattern T

● Use parameter flags. When designing the program and its command line, use parameter flags (for example, -f input_file) rather than relying on param

3. Click Help for instructions on how to complete the task definition form. 4. Complete the task definition form. 5. Click Save to create the task.

Typically, you enter the command line as a combination of fixed text and variables defined by GenePattern. This allows the command line to be independ

Writing MATLAB Modules for GenePattern If you are writing MATLAB code to be invoked as a GenePattern task, follow the guidelines in Writing Modules

● Distributing Your MATLAB Code ● Example: Deploying a Compiled MATLAB Application Two Approaches: Direct and Compiled You can invoke a MATLAB executa