Hi John,

As I specified it in the "edit" of my first message, I have this error
only if I run groomer with a command line in another xml file
surrounding by other command. When I run groomer alone with the
original xml, it works fine, so no problem with the PYTHONPATH.
 But when I use this :
<command>
                #if $fastq_format == "illumina"
        blabla_No_python_command
                #else
        python /data/galaxy-dist/tools/fastq/fastq_groomer.py
'tmp.fastqcssanger' 'cssanger' '$output' 'illumina' 'ascii'
'dont_summarize_input'
                #end if
</command>

It doesn't work.

I've checked the files contained in job_working_directory. A shell
script is generated for my job and it begin with these lines :

#!/bin/sh

GALAXY_SLOTS="1"; export GALAXY_SLOTS;
export GALAXY_SLOTS
GALAXY_LIB="None"
if [ "$GALAXY_LIB" != "None" ]; then
    if [ -n "$PYTHONPATH" ]; then
        PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"
    else
        PYTHONPATH="$GALAXY_LIB"
    fi
    export PYTHONPATH
fi



So, with the run of groomer alone the line GALAXY_LIB is equal to
"/data/galaxy/galaxy-dist/lib", but here with the run of groomer with
a command line with another job the GALAXY_LIB is set to "None"!!!
I don't understand why.

For the moment, to surround the problem, I've explicitly specified the
GALAXY_LIB path int the xml command before the command line wich run
python fastq_groomer.py and it works but I'm aware that is not
beautiful.

Finally I'm using a local jobrunner.

Thanks for your help
Julie

P.S : we use such command because we build a workflow where the
quality format of the fastq must be invisible for the users.

2014-07-03 19:48 GMT+02:00 John Chilton <jmchil...@gmail.com>:
> Hello Julie,
>
>   This is odd - sorry.
>
>   I might be worth uninstalling and re-installing this in the tool
> shed admin options - in particular ensure you install tool
> dependencies and that this installation process succeeds.
>
>   Otherwise -  it might be worth trying to put some debug statements
> in the fastq groomer tool to try to track down the problem. Here
> (https://gist.github.com/jmchilton/2d61f7ab81d99a0f02fc) is a diff to
> have that tool write out the run-time value  PYTHONPATH to Galaxy's
> home directory - it might be worth running a job, finding the output,
> setting PYTHONPATH to that value on the compute node and attempting to
> just import it directly.
>
> cd $HOME; python -c "import galaxy.sequences.fastq"
>
>   Out of curiosity - what job runner are you using (local, DRMAA, etc...)?
>
> -John
>
> On Tue, Jul 1, 2014 at 4:50 AM, julie dubois <dubju...@gmail.com> wrote:
>> Hi,
>> I've this error message when I run groomer.
>>
>> My local instance of galaxy runs on a python virtualenv (python 2.7)
>> and I have make the latest update with : hg pull -u.
>>
>> I've verified and this library is present in my
>> galaxy-dist/lib/galaxy_utils/sequence directory.
>>
>> I've found no other idea than the update on this forum to run groomer
>> correctly, any other idea ?
>>
>> Thanks.
>> Julie
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