Respected Sir,

I don't think so that problem is in tool, because when I run same tool of normal terminal, it generate output.

What I am thinking is:

Consider Galaxy is running from its own directory, my files are in /home/user/Documents/

While uploading file, I am choosing for "Link to files without copying to galaxy".

Due to this command is able to link files, but other files which are listed in fileList.tab are not able to recognized by galaxy

because

- files are in Documents

- Galaxy running its command from other location.

In other side, when I am running through terminal

- I go to /home/user/Documents/

then run commands, hence all files listed in fileList.tab are accessible to software.

On Thu, Feb 27, 2014 at 3:32 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:

On Thu, Feb 27, 2014 at 9:32 AM, do kadya <dokadya@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