MATLAB APPLICATION DEPLOYMENT - WEB EXAMPLE GUIDE Manuale Utente Scaricare il pdf (Pagina 4)

Introduction

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

through the

GenePattern Tutorial before reading the more detailed information in this guide.

As a programmer, you generally work with GenePattern in one of two ways:

● Creating GenePattern tasks. Each GenePattern task invokes a program that executes a desired function. You

can use any language to write a program that can then be invoked as a GenePattern task. For more information,

see:

▪

Writing Modules for GenePattern: This section provides tips for writing code that will be invoked as a

GenePattern task.

▪

Writing MATLAB Modules for GenePattern: This section describes how to address MATLAB licensing and

distribution issues. Read this section if you are writing MATLAB code that will be invoked as a GenePattern

task.

● Accessing GenePattern from Java, MATLAB, or R. GenePattern libraries for these three programming

environments make it easy for your applications to run GenePattern tasks and retrieve analysis results. Each

library supports arbitrary scripting, access to GenePattern modules via function calls, and development of new

methodologies that combine modules in arbitrarily complex combinations. For more information, see:

▪ Using GenePattern from Java

▪

Using GenePattern from MATLAB

▪ Using GenePattern from R

Writing Modules for GenePattern

Creating a GenePattern task is a two-step process:

1. Write a program that executes the desired function. For more information, see Guidelines for Writing Programs

for GenePattern Modules

2. Use the GenePattern Web Client to create a GenePattern task that invokes the program that you have written.

For more information, see

Creating Tasks.

Guidelines for Writing Programs for GenePattern Modules

When writing a program that will be run as a GenePattern task, keep in mind the following:

● Use the programming language of your choice. You can write the program in the language of your choice.

You can use a compiled language, such as C, to create an executable or you can use a scripting language, such

as Perl, to create a script that is run by an interpreter.

● Write messages to standard error and standard output. GenePattern tasks are run on the server. The user

provides arguments and retrieves results, but does not interact during task execution. If necessary, write normal

output to standard output (stdout) and error messages to standard error (stderr); avoid writing error messages to

standard output. GenePattern captures stdout and stderr in log files, which can be retrieved by the user.

● Write output files to the current working directory. When a task completes, GenePattern displays the output

files that are in the current working directory. Files written to other locations are not displayed as task output files

(otherwise known as analysis result files).

● Read module data files from <libdir>. If your module needs to read from any data files which are part of the

module (rather than user input), it will need to know the directory where the module lives on the server; that is,

<libdir>.

● Read and write standard GenePattern file formats. When reading and writing data files, you generally want to

use the standard GenePattern file formats, as described in

File Formats. This makes it easier for users to

analyze their data using a combination of GenePattern modules. If you choose to use your own unique file

formats, be aware that other GenePattern modules will not be able to read those files.

For Java, MATLAB, and R, GenePattern provides libraries that include methods for reading and writing

GenePattern files (such as res, gct, and odf files). These libraries are designed for accessing GenePattern from

the Java, MATLAB, and R environments, but are also useful when writing modules to be invoked by

GenePattern. For instructions on downloading the libraries, see

Using GenePattern from Java, Using

GenePattern from MATLAB

, or Using GenePattern from R.

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MATLAB APPLICATION DEPLOYMENT - WEB EXAMPLE GUIDE Manuale Utente Pagina 4

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