Hello Galaxy community, I am new to Galaxy and had a question while developing my local instance and running my files through the local instance.
What I have tried so far:
So I created a local Galaxy instance with default configurations, and after becoming an admin following the guidelines in this tutorial: Get Galaxy I created a simple workflow by following this tutorial while I am still an admin in my local instance Create and share workflows in Galaxy - YouTube
and wanted to share this with my end user as a service for RNA-Seq analysis keeping these rules in mind Ten Simple Rules for Setting up a Galaxy Instance as a Service
Challenge:
But once I log out of the web instance in which I was the admin and log back in as a non admin user into the same local instance I created, I am not able to see the workflow I created. I guess I was assuming that once the workflow is created, anyone who has access to the local instance can just access the workflow and run their files through it.
To summarize:
I am interested in sharing this workflow with my end user so that they can simply open up this galaxy instance, input their files and the files run through the galaxy instance which gives them the desired output in the end! How do I accomplish this?
Share the workflow with all other users working on that same Galaxy server by publishing it.
Publishing creates a URL that can be shared with others, but also places the shared object directly under “Shared Data > Workflows”.All users working on that same Galaxy server will have access, and they can import and use the workflow in their own accounts.
Any account can “publish” into Shared Data: 1) Histories (and the Datasets inside of them), 2) Workflows, 3) Visualizations, 4) Pages.
Any account can also “share” work. Directly with the other person’s account email address, or by generating a share link URL and giving that URL to them (however you communicate: text, slack, email, etc)
Only admin accounts can add data into Shared Data: 1) Data Libraries. It is a different way of organizing commonly used data and can save you some storage space since data in a Data Library imported by a user is just a linked clone of the original dataset.
Workflows do not consume any space at all in any account in terms of quota usage, but these files of course do consume a tiny amount of space on disk. That said, Datasets and Histories are much larger and matter more in terms of managing the overall disk size of your instance.
Note: The FAQs and Tutorials show a slightly older version of Galaxy (the application changes fast!), but you should still be able to find the “Share or Publish” form for any Galaxy object and share/set permissions how you would prefer to. In practical terms, you might want to not grant editing permissions the workflows if you want the users to import and run the workflow exactly how it is published. The Webinar series was new this month, and includes operations using the most current Galaxy version.
Thank you for your reply, I was able to implement and publish a workflow and solve the problem!!
There was just one concern I had post implementation. So once I access the published workflow and hit Run, the “central panel” pops up which allow me to configure and launch the workflow. I was wondering if there is a way that I can just avoid this step for the end user as I just want them(the end user) to hit Run after their files are loaded as input in the beginning and just receive the processed files from the pipeline as the output without making any changes to my created/published RNA-Seq workflow (basically automate this process as much as possible for the end user)