MATLAB APPLICATION DEPLOYMENT - WEB EXAMPLE GUIDE Manuale Utente Scaricare il pdf (Pagina 5)

● Use parameter flags. When designing the program and its command line, use parameter flags (for example, -f

input_file) rather than relying on parameter positions. Parameter flags allow users to build command lines with

variable numbers of arguments, which makes it easy to omit optional parameters.

When writing R code, if you have optional input parameters on the command line, you must use named rather

than positional parameters in the command line definition; for example:

input.filename=<input.filename>. If you name all of the parameters, then you can use ellipses

rather than listing the parameter names in the function definition (for example:

myfunc <-

function(...)

) at the expense of clarity in documenting input parameters.

● Process all parameters as strings. All command line parameters are passed to your code as strings, even if a

parameter is apparently numeric. If your code expects a numeric argument, explicitly convert the string argument

to a number; for example, as.integer(arg).

● Avoid absolute pathnames. When writing code to be used with GenePattern, avoid absolute pathnames. For

example, in perl, specify the interpreter on the command line rather than embedding the interpreter in the script;

that is, use the command line “

perl myscript” rather than including ”#!/usr/bin/perl” as the first line

of the

myscript.pl file.

● Avoid Windows forbidden filenames. Machines running Windows cannot accept files with the following

names, regardless of the file extension: con, prn, aux, nul, com1, com2, com3, com4, lpt1, lpt2, lpt3. For cross-

platform compatibility, avoid files with these names.

● Adapting R code. When you create a task in GenePattern, you specify the command line that invokes the

program that performs the desired function. Generally, the command line includes arguments, such as the

parameters for the algorithm and the data file to analyze. For example, the following command line invokes the

myfunc() function in the R script named myscript.R, passing a single parameter, input.filename:

<R> <libdir>myscript.R myfunc <input.filename>

Calling R script from a command line is possible, but generally not useful because you cannot pass arguments to

the script. To pass arguments to your R code, create a function. For example:

myfunc <- function ( input.filename )

... (your R-code here)

Creating Tasks

To create a task that invokes the program that you have written, use the GenePattern Web Client:

1. Display the Web Client home page. (If you are unfamiliar with the GenePattern Web Client, see the

Web Client

Guide

2. Open the task definition form in one of the following ways:

▪ Click

Create in the Tasks pane.

▪ Click

create task under Tasks and Pipelines in the right column.

▪ View or edit a task and use the Clone button to create an identical task.

The Web Client displays the task definition form:

1 2 3 4 5 6 7 8 9 10 ... 21 22

Nessun commento

MATLAB APPLICATION DEPLOYMENT - WEB EXAMPLE GUIDE Manuale Utente Pagina 5