MATLAB APPLICATION DEPLOYMENT - WEB EXAMPLE GUIDE Manuale Utente Scaricare il pdf (Pagina 7)

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

allows the command line to be independent of the operating environment and allows different values to be

specified at different invocations of the command. This command line uses the following variables:

▪ <perl> represents the full path to the Perl installation used by GenePattern.

Similar variables are available for <java> and <R>. If your program was run by another interpreter, such a

Python or LISP, you could use an absolute pathname (for example, /usr/bin/python) or create a new

GenePattern variable for the interpreter pathname (for example, python=/usr/bin/python) in the

GenePatternServer/resources/genepattern.properties file. If your program was an

executable file, you would not need an interpreter, so would not need this variable.

▪ <libdir> represents the full path to the directory that contains the files for this task, including the program file.

▪ The Perl script,

log_transform.pl, expects two parameters, an input file and an output file name: -F

<input.filename> -o <output.file>

. When your program has parameters, you include them in

the command line and also define them in the Parameters field, which appears below.

5. Enter the following information in the next few fields:

▪ task type: Preprocess & Utilities

▪ CPU: Any

▪ Operating system: Any

▪ Language: Perl

▪ Version comment: A brief note of what is special or interesting about this version.

▪ output description: Select gct from the list of formats.

The

output description field defines all file formats used by your module. To select multiple formats, use

Shift+click (Option+click or Apple+click). Include both input and output file formats in this list.

6. Use the

Support files field to upload your program, any other files needed to execute the task, and

documentation for the task (a file with a text extension, such as .pdf, .doc, or .txt):

1. Click the

Browse button at the end of the first line in the Support files field. The Web Client displays the File

Upload window.

2. Navigate to the gp_tutorial_files/log_transform directory, select the file

log_transform.pl, and click Open. This is the script that implements the task.

3. Click the

Browse button at the end of the second line in the Support files field. The Web Client displays the

File Upload window.

4. Select the file LogTransform.pdf and click Open. This is the documentation for the task. When a

GenePattern user displays your task and clicks the

Help button, GenePattern displays the support file that

has a text extension (such as .pdf .doc, or .txt).

7. Use the

Parameters field to describe your two program parameters: input.filename and output.file. The

parameter names and descriptions that GenePattern displays when a user runs your task are the parameter

names and descriptions that you provide here.

In the first row of the

Parameters field, enter the following information for input.filename:

▪ name: input.filename

▪ description: The dataset to be transformed (gct format).

▪ type: choose input file

▪ fileFormat: choose gct

In the second row, enter the following information for output.file:

▪ name: output.file

▪ description: The name of the new transformed file.

▪ type: choose text (this is a name that the user enters)

8. Click

save. The Web Client displays a message informing you that the task has been saved.

9. Run the task to confirm that it has been added to the GenePattern server correctly.

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MATLAB APPLICATION DEPLOYMENT - WEB EXAMPLE GUIDE Manuale Utente Pagina 7

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