On Thu, Feb 27, 2014 at 9:32 AM, do kadya <doka...@gmail.com> wrote:
> Hi,
> Thank You for your kind reply.
>
> I am having problem in running command in Galaxy.
> my current command:
>
> <tool_name>     <file_having_multiple_file_name_tab_delimited.txt or .tab>
> <file1.bam>   <file2.bam>
>
> /usr/bin/x_tool  fileList.tab  file1.bam  file2.bam
>
> I have created xml file so that i can run this command through Galaxy. Its
> showing error:
> Can't call method "print" on an undefined value at
> /usr/local/share/perl/5.14.2/GTF/tool_x/Calc.pm line 110.
>
> When I am running same command from terminal, its working.
>
> From these I have hypothesize:
> - Galaxy is having different path to run its script, and different file
> name.
> - FileList.tab contains list of other files which present in same folder.
> - As tool is not able to search those files, may be galaxy is having
> different path where it run the command.
> -------
> While uploading file, I am using user defined path so that galaxy will not
> create replica of it,
> hence when I see error file of Galaxy output (by clicking on (i) symbol )
> its showing the same path where all my files are located.

Normally tool development questions are on the galaxy-dev list
(CC'd).

It sounds like your problem is inside your own Perl script?
Perhaps within Galaxy there is a problem with the Perl
environment variables defining where to find Perl libraries...

Peter
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