Galaxy + User Program Unable To Locate Files

Question: Galaxy + User Program Unable To Locate Files

4.8 years ago by

do kadya • 130

do kadya • 130 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. - 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.

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modified 4.8 years ago by Peter Cock • 1.4k • written 4.8 years ago by do kadya • 130

4.8 years ago by

Peter Cock • 1.4k

European Union

Peter Cock • 1.4k wrote:

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

ADD COMMENT • link written 4.8 years ago by Peter Cock • 1.4k

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.

ADD REPLY • link written 4.8 years ago by do kadya • 130

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

ADD REPLY • link written 4.8 years ago by Peter Cock • 1.4k

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