Hi Peter

I removed the unnecessary code.

If I run the tool with just a couple of inputs I see entries in the log 
files either from galaxy.jobs.runners.drmaa or from 
galaxy.jobs.runners.local that the job is being dispatched as normal.

Unfortunately there is no sign of the job in the log files when using 
more input files.

The command line that is supposed to be run is:

bash home/galaxy/galaxy-dist/tools/vcf_processing/vcf_to_fasta.sh 
/galaxy/database/files/042/dataset_42275.dat 40 10 50 0 40 0.9 20 

the first dat file being the output and the ones at the end being a 
comma separated list of the input files. On the command line this 
command works with much longer input files lists.

Any ideas? Or is there a better practice to pass a large number of input 
files to a bash script?


On 22/04/14 15:26, Peter Cock wrote:
> On Tue, Apr 22, 2014 at 3:02 PM, Ulf Schaefer <ulf.schae...@phe.gov.uk> wrote:
>> Dear all
>> I am using this control to allow the user to input multiple files:
>> <param name="input_vcfs" type="data" multiple="true" format="vcf"
>> label="Input VCF file(s)" />
>> and I am using this for loop in the cheetah code to access the control:
>> <command interpreter="bash">
>> script.sh
>> ...
>> #for $i, $input_vcf in enumerate( $input_vcfs ):
>>       "${input_vcf}",
>> #end for
>> </command>
> The $i and enumerate seem unnecessary here.
>> It appears that when a user selects many files (25 in this case) the
>> bash command in the command tag never gets executed. Therefore the job
>> is never queued. The history item shows 'Waiting to run' indefinitely.
>> Calling the script.sh manually with 25 input files works fine.
>> Any hint as to how to debug this would be greatly appreciated.
>> Thanks a lot
>> Ulf
> Can you see anything in the log about the job, and in particular
> the command line it would attempt to run?
> Peter

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