On Dec 14, 2011, at 9:45 PM, Roger Ngo wrote:

> Hi, I have a perl script which executes a Java JAR file located in 
> tool-data/shared/jars/ and this Jar file at one point executes 2 other binary 
> programs during its job process. These 2 programs are located in the same 
> directory as the JAR file.
> 
> I am getting errors in Galaxy saying "No such file or directory" when these 2 
> external programs are called. I am assuming this is the case because they are 
> not located in current working directory of the current Galaxy job process. 
> 
> Is there a way to somehow redirect Galaxy into the correct directory where 
> the binary files are located?

Hi Roger,

The simplest solution would be to place the subsequent binaries somewhere else 
that's on $PATH (or put tool-data/shared/jars/ on $PATH - you could even do 
this right in the perl script).  You could also modify the code in the jar to 
look in the same directory as the jar, assuming you have the Java source.

--nate

> Thanks.
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