juan perin wrote:
Actually, i did not want to use file staging. I am running from my home directory which is visible on all nodes, and has plenty of space for my needs. I'm guessing I did something in the config to activate file staging, in which case that would explain the error that shouldn't be. I didn't read closely enough, but I set:
# The PBS options are described in detail in the Galaxy Configuration section of # the ClusteringGalaxy Wiki, and are only necessary when using file staging. pbs_application_server = variome pbs_stage_path = /home/perin/galaxy-dist/database/tmp pbs_dataset_server = variome
which obviously caused issues as a result. Commenting this back cleared it up, but introduced another issue, where the nodes apparently don't see the binary it is trying to run. I was assuming that the binaries were located in the home directory I was running from, but now see that they are actually in /usr/local/bin/etc... I'm not sure where this is set, but assume it was done sometime during the setup.sh process. Is there a way I can specify this install location, or change it anywhere? I can copy the binaries over to the nodes, but would prefer to host them in a shared place. Is there a way to change Galaxy so that it looks in say "/share/apps/bin/" instead of /usr/local/bin ?
Do you mean the binaries for the dependencies? If so, they are expected to be found on the $PATH, so if that's consistent on the Galaxy server and the nodes, you should be okay. Otherwise, I'm not sure which binaries you're referring to.