Re: [galaxy-dev] workflow representation and execution...

2011-03-30 Thread Dannon Baker
Hi Kostas, Workflows are saved in the database. If you're looking for an external representation you can generate one by going to 'Download or Export' in an individual workflow's menu in the main workflows list. The download option there gives a JSON representation of the workflow that can

Re: [galaxy-dev] workflow representation and execution...

2011-03-30 Thread Kostas Karasavvas
Thank you Dannon! As far as where the jobs will run, it is definitely possible that multiple jobs in a single workflow will execute on different nodes. Good to know. I assume that currently that is not happening though, right? If yes, is it in your immediate plans? Cheers, Kostas

Re: [galaxy-dev] workflow representation and execution...

2011-03-30 Thread Glen Beane
On Mar 30, 2011, at 6:01 AM, Kostas Karasavvas wrote: Thank you Dannon! As far as where the jobs will run, it is definitely possible that multiple jobs in a single workflow will execute on different nodes. Good to know. I assume that currently that is not happening though, right? If

Re: [galaxy-dev] workflow representation and execution...

2011-03-30 Thread Kostas Karasavvas
Hi Glen, Good to know. I assume that currently that is not happening though, right? If yes, is it in your immediate plans? It should happen now - each step in the workflow would get submitted as a separate job to the cluster.  At that point it is up to the job scheduler and not Galaxy to

Re: [galaxy-dev] workflow representation and execution...

2011-03-30 Thread Glen Beane
On Mar 30, 2011, at 8:34 AM, Kostas Karasavvas wrote: Hi Glen, Good to know. I assume that currently that is not happening though, right? If yes, is it in your immediate plans? It should happen now - each step in the workflow would get submitted as a separate job to the cluster. At

Re: [galaxy-dev] workflow representation and execution...

2011-03-30 Thread Kostas Karasavvas
Hi Glen, All is clear now. Thanks for the info! :) K. the job should copy its output files into the Galaxy database/files directory before it terminates.  So assuming you are not using data staging and the database directory is shared via NFS, then the next tool will read the files from