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
>
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Reply via email to