Hello, using galaxy for the first time on AWS through the genomics virtual lab on cloudlaunch. I understand that I cannot use the same username as when I use the public servers but my question is, how do I then use a workflow?
I want to be able to have a workflow I can run every time I run galaxy on AWS but it seems that it creates a new blank server every time with no way to save a workflow for next time. Is this way of using galaxy only for exploratory analysis?
Thanks
Workflows can be downloaded and uploaded through the Galaxy interface. Is that what you need?
Look under the masthead section “Workflows”. There is an upload/import icon at the top of the page and any workflows that are yours will have “download” as an option listed on the per-workflow pull-down menu.
Hope that helps!
Post that may be of interest (customizing/saving cloud AMI images, etc):
Thanks for the reply,
That is how I would do on the public galaxy server (usegalaxy.org), because I can login into my main user and use workflows I have created. However, while using galaxy on AWS, each time I launch it, it is a “different” galaxy server, so I cannot login with my main username that I use for the usegalaxy.org. and therefore can’t pull workflows from the normal username. Does that clarify my question?
Try downloading a copy of your workflow from usegalaxy.org. It will be in a file that ends with the extension .ga. That can then be uploaded to the cloud server into your new account.
The first time you open the workflow in the editor, warnings will come up if any tools/tool version are a mismatch for what is already installed on the default server. You can update tools in the workflow, install new tools on the server, etc until things match up. Installing new tool indexes is also possible.
Once you have customized your cloud server (if you need to), you can save an AMI image for reuse. This will cost money to maintain, so if you decide to do this, keeping the image as small as possible would be a good idea (save a copy that does not include full analysis, just what you need to start up a new analysis – permanently delete non-reusable account data, etc).
Workflow objects themselves use up very little space, so you could keep yours in the AMI. Or, download a copy of the workflow configured to work with the GVL default install or your custom AMI. Saving a backup copy is good idea anyway.
Just tried downloading a copy of a simple workflow and uploading to cloud server and it seems to work well! Thanks for the info!
Great news – very glad it worked out 