Hi Marine If I use the xml file as you have posted in this e-mail, it works. ie it works up to the error message: "An error occurred running this job: /bin/sh: /home/myName/myToolRepository/bin/myTool: not found " I don't get the cheetah error you show. Are you sure, you are using the same xml file? Regards, Hans On 05/30/2012 06:06 PM, Marine Rohmer wrote:
Ok, when I remove "interpreter = C++" from <command>, and keep it empty or write "interpreter = "bash" instead, I have no more this error message. Galaxy says "The following job has been successfully added to the queue",and I can show its progression on the history. Thank you Ross !
But now I have a new error message that I can't solve : An error occurred running this job: /failure preparing job /Details are: Traceback (most recent call last): File "/home/myName/work/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 59, in run_job job_wrapper.prepare() File "/home/myName/work/galaxy-dist/lib/galaxy/jobs/__init__.py", line 429, in prepare self.command_line = self.tool.build_command_line( param_dict ) File "/home/myName/work/galaxy-dist/lib/galaxy/tools/__init__.py", line 1971, in build_command_line command_line = fill_template( self.command, context=param_dict ) File "/home/myName/work/galaxy-dist/lib/galaxy/util/template.py", line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File "/home/myName/work/galaxy-dist/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs4.egg/Cheetah/Template.py", line 1004, in __str__ return getattr(self, mainMethName)() File cheetah "cheetah_DynamicallyCompiledCheetahTemplate_1338392112_91_81444.py", line 83, in respond NotFound: cannot find 'HOME'
I've tried to put an erroneous path/to/myTool in <command> in order to see if my original path is right. It indeed gives me another error message saying "An error occurred running this job: //bin/sh: 1: path/to/myTool: not found/" , which makes sense since the path is erroneous.
I've also tried to put some erroneous data in the XML file (for example wrong names in <param>) to see if it influences the error message, but I still have the same. (that is to say : NotFound: cannot find 'HOME')
With Hans' help, my XML file is bettered that way :
<tool id="mytool" name="My Tool"> <description> description </description> <command > /home/myName/myToolRepository/bin/myTool -i = $genome_index -r = $input -k = $kmer_length </command>
<inputs> <param name="genome_index" type="select" label="Genome index"> <option value="E.coli"> /path/to/indexEcoli </option> <option value="Human"> path/to/indexHuman </option> </param>
<param format="txt, raw, doc, fastq" name="input" type="data" label="Source File" help="Select a file"/>
<param name="kmer_length" type="integer" min="15" max="150" value="21" label="k-mer length"/> </inputs>
<outputs> <data format="sam" name="crac_outfile" label="crac outfile" /> </outputs> <tests> <test> </test> </tests> <help> </help> </tool>
Regards, Marine