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

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