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.c...@googlemail.com>wrote:

> 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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