Re: [galaxy-dev] ImportError: No module named galaxy
On Nov 2, 2011, at 4:45 PM, Oren Livne wrote: Dear Nate, My PYTHONPATH is already set to this value. Hi Oren, Is it exported? If it's set to Galaxy's lib directory, it should not be possible that the galaxy module can't be found. --nate Best, 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] ImportError: No module named galaxy
Dear Nate, My PYTHONPATH is already set to this value. Best, 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] ImportError: No module named galaxy
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: http://lists.bx.psu.edu/ ___ 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: http://lists.bx.psu.edu/
[galaxy-dev] ImportError: No module named galaxy
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. 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 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: http://lists.bx.psu.edu/
