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
While uploading file, I am choosing for "Link to files without copying to
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
- 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
On Thu, Feb 27, 2014 at 3:32 PM, Peter Cock <p.j.a.cock(a)googlemail.com>wrote:
On Thu, Feb 27, 2014 at 9:32 AM, do kadya <dokadya(a)gmail.com>
> 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
> <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.
> 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
> - 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
> 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
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...