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...)?
On Tue, Jul 1, 2014 at 4:50 AM, julie dubois <dubju...@gmail.com> wrote:
> 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 ?
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