Question: load workflow create history in config?
0
gravatar for eric
18 months ago by
eric0
UC Berkeley
eric0 wrote:

Is there a way to load workflows and/or create a new history from a config file, without using the GUI or API (i.e. pre-runtime)?

galaxy • 404 views
ADD COMMENTlink modified 18 months ago • written 18 months ago by eric0

Could you please describe your use case a bit?

ADD REPLYlink written 18 months ago by Martin Čech ♦♦ 4.9k

Thanks for the reply. I'm trying to install a workflow and create a named history without using an api. This is to make a setup process for my application to require less steps. For example, I can generally install custom tools by just referencing them in galaxy.ini (tool_config_file=) Can I install workflows in the same way?

Thanks

ADD REPLYlink written 18 months ago by eric0

I understand what you want to do, I am curious about why you want to do it (ie what does your application do).

afaik you cannot install workflows this way. And you can load tools into galaxy by referring to them in configs, but you won't have the dependencies installed thus losing reproducibility I believe.

ADD REPLYlink written 18 months ago by Martin Čech ♦♦ 4.9k

Thanks. I'm writing a jbrowse plugin that executes a galaxy workflow. Trying to figure out how to setup an easy example.

ADD REPLYlink written 18 months ago by eric0

If you are going to execute the workflow anyway why are you avoiding having Galaxy up for the installation/loading?

ADD REPLYlink written 18 months ago by Martin Čech ♦♦ 4.9k

I do assume that the user has to setup galaxy, jbrowse, and our sample workflows. Just trying to make that process easier, if I can automate some of it (or all of it).

ADD REPLYlink written 18 months ago by eric0

Giving the user an ansible playbook to execute all of this might be the simplest approach here. Depends on how tech savvy your users are.

ADD REPLYlink written 18 months ago by Martin Čech ♦♦ 4.9k

ok. I'll have to look into it. thanks.

ADD REPLYlink written 18 months ago by eric0
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