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 ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev 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/