Oren Livne wrote:

Dear All,

I am running the example_watcher_folder.py API script and it intermittently fails to run a workflow on a file dropped into the import directory (the file is imported and the workflow starts running, but its jobs hang or fail). Galaxy uses a condor dramaa job runner. When I look at the galaxy script being run by condor, it sets the PYTHONPATH and then executes the following command, which also fails at the command line.

Hi Oren,

Is the intermittent failure the same error was below?

galaxy@vm-debian:~/galaxy-dist$ python /home/galaxy/galaxy-dist/tools/filters/sorter.py --input=/tmp/galaxy/datafiles/000/dataset_105.dat --out_file1=/tmp/galaxy/datafiles/000/dataset_106.dat --column=7 --style=num --order=DESC Traceback (most recent call last): File "/home/galaxy/galaxy-dist/tools/filters/sorter.py", line 15, in <module> from galaxy import eggs ImportError: No module named galaxy

This won't work from the command line unless you set PYTHONPATH the same way that the framework does (i.e. PYTHONPATH=~/galaxy-dist/lib).

--nate

How can I resolve this error? I would like to be able to test such commands at the command line, as well as ensure that galaxy workflows run reliably.

Thanks, Oren ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:

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