MATLAB APPLICATION DEPLOYMENT - WEB EXAMPLE GUIDE Manuale Utente Scaricare il pdf (Pagina 6)

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.

Note: By adding a task, a user can execute arbitrary code on the GenePattern server. Because arbitrary code may

include malicious code, consider taking precautions to protect your server: for example, employing virus scanner

software and restricting access to appropriately privileged (non-root) users. For more information about securing your

server, see

Securing the Server in the Web Client Guide.

Tutorial: Creating a Task

While creating a task is not difficult, it can be intimidating the first time. The following brief tutorial walks you through

the process by helping you create a task named log_transform. The program invoked by this task is a Perl

script,

gp_tutorial_files/log_transform/log_transform.pl, which log-transforms all positive

values in a data set and sets all negative or zero values to zero. This Perl script is part of the GenePattern tutorial

data set, which is downloaded during a full installation of GenePattern and is also available on the

GenePattern web

site

To create the

log_transform task:

1. Display the Web Client home page.

2. In the Tasks pane, click

Create. The Web Client displays the task definition form. (The task definition form, with

the tutorial data filled in, appears at the end of the procedure.)

3. Enter the following information in the first few fields:

▪ Name: LogTransform

▪ Description: Log transform a data (gct) file.

▪ Author: Your name and affiliation.

▪ Privacy: Select private. This means that only you (users logged in using the user name in the

Owner field)

can view and run the task. Public allows all users connected to this server to view and run the task.

▪ Quality level: Select preproduction. This indicates that you have finished development, but are not yet

ready for production.

4. Enter the following text in the

command line field (if you are working online, cut and paste this text into the field):

<perl> <libdir>log_transform.pl -F <input.filename> -o <output.file>

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MATLAB APPLICATION DEPLOYMENT - WEB EXAMPLE GUIDE Manuale Utente Pagina 6