Galaxy + user program unable to locate files
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.
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
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
On Thu, Feb 27, 2014 at 4:20 PM, do kadya <dokadya@gmail.com> wrote:
I don't think so that problem is in tool, because when I run same tool of normal terminal, it generate output.
This is why I was asking about Perl environment variables - they may be different compared to when you run the tool. For example, is Galaxy run as a different Linux user? Peter
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Peter Cock