Hi all- I'm using https://github.com/ebi-gene-expression-group/galaxy-workflow-executor to try and run a workflow via the API from the command line. This works fine on our local Galaxy, but on usegalaxy.eu it stops after uploading the first input dataset with
Failed due to ('Connection aborted.', ConnectionResetError(104, 'Connection reset by peer'))
I can consult @pcm32 on the code, but is there something I need to do (other than setting the API key which I've done) to enable successful running via the API? I'm pointing at "https://usegalaxy.eu".
we need to schedule the job, so spades requests a set amount of memory before it can be scheduled.
We do not have a good, accurate model yet for how much memory spades uses based on input settings, so, we set it to a high number that can accommodate the full range of assemblies being conducted on EU.
Unfortunately that means for even small assemblies, spades is a "big" job that is hard to find space for in our a queue.
queuedhave been actually resubmitted because they crashed.
Regarding my Query Tabular issue, I found a workaround: when I rerun it, if I expand the Table Options for each input table when re-invoking the tool then the options are correctly selected. If I don't they seem to be lost more likely than not. See e.g.
where dataset 7 was created from datasets 1-6. Dataset 8 failed when the "rerun" button was pressed followed immediately by the Execute button. Using the "circle-i" button, inspection shows that
Use first line as column names is set to false for all tables for Dataset 8 whereas it was set to true for all tables for Dataset 7.
Right now I am thwarted in my effort to set up another galaxy instance to reproduce it there.