Yesterday I submitted six human RNA-seq alignment jobs to galaxy server. One day after the status for two jobs is "This job is waiting to run" and the status for the other four jobs is "This is a new dataset and not all of its data are available yet". I'm now considering to submit these jobs manually to Stampede servers to run but I don't know how to get access to Stampede from galaxy. I'll be very grateful if you can direct me to the right place to do this.
The target cluster can be selected when using the tool form option: Job Resource Parameters. Not all tools have this option but most mapping tools do. This FAQ explains and also covers job concurrency limits (which it sounds like you hit). https://galaxyproject.org/main/
Jobs cannot be submitted manually (line command?) to resources when using Galaxy Main at https://usegalaxy.org and the other public Galaxy servers that I am aware of.
That said, it looks like your HISAT2 jobs completed but I might be looking at the wrong account. If you want to send an email to email@example.com from your registered account, and note the history name and job numbers that are still queued after a day, we can take a look. The most common reason for jobs to not run is due to problems with the inputs. Include a link to this post and make sure the input and output datasets are left undeleted.
- Datasets and how jobs execute https://galaxyproject.org/support/#datasets-and-histories
- Troubleshooting, job errors, input help https://galaxyproject.org/support/#troubleshooting
The Galaxy Main server is undergoing many changes for the 18.05 pre-release testing. Most functions are fine, but you could also consider working at one of our mirrors (still running the stable 18.01 release): https://usegalaxy.eu or https://usegalaxy.org.au. Or, at another public Galaxy: https://galaxyproject.org/public-galaxy-servers/. Running many jobs at once will still result in some of them being queued at any of these servers -- how long depends on overall load and any concurrency limits in place.
Thanks, Jen, Galaxy team