9:02 a.m.
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 <jmchilton(a)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 <dubjulie(a)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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