Urgent: Help needed regarding usegalaxy.eu and usegalaxy.org

Hi. I recently tried to replicate the results of a Galaxy tutorial for variant analysis using usegalaxy.eu server.

But when almost half of the analysis was done, I came to know that some tools used in the tutorial are only found at usegalaxy.org server. In fact all the analysis was done on usegalaxy.org server. Now I am doing again all the analysis on usegalaxy.org.

Is there any way that I can copy all the completed steps of usegalaxy.eu on usegalaxy.org, so that I don’t have to run again all the steps, coz it is taking so much time for me.

Can please someone guide me about this problem? Or is there is any way I can “transfer” (use) the tools found on usegalaxy.org to usegalaxy.eu server?

Waiting for your kind responses,

Regards,
~Huzaifa

2 Likes

Hi @hhuziii

Seems your topic post was missed by the community. In case you still need help, or someone else wants more clarification about your questions later on (are likely things other new Galaxy users are interested in) … replies are below. Thanks!


Question 1: Why are not all tools in each GTN tutorial hosted at all public Galaxy servers? How can I find out which server to use, per tutorial?
Help 1: Servers host different tools. You can check to see which public Galaxy servers are good choices per tutorial. These can change over time, and a server may actually host the tools but not be listed because the tool version was updated (meaning, the tool can be used but perhaps not exactly as described in the tutorial). How to use an updated tool is usually possible to figure out – but if you are not sure, can always ask – here (new topic) or even better at the GTN Gitter chat: https://gitter.im/Galaxy-Training-Network/Lobby (asking there may even get the tutorial updated).
Notes: The particular tutorial you reference has a dedicated Docker image and isn’t technically/exactly supported by any public Galaxy server – but you may still be able to use it at some of them.
Screenshots and more info below:

Screenshot of the Hands-on for the tutorial you mention (the “globe” icon menu is also here, for each tutorial):


Question 2: Can I personally move data from one Galaxy server to another? Including public Galaxy servers?
Help 2: Yes. Datasets, Histories, Workflows can all be transferred directly (or downloaded to a file then uploaded to a public/private Galaxy again). For Datasets, click on the “disk” icon in the expanded dataset, copy the URL, and paste that into the Upload tool at the other server. For entire Histories, create a History archive (option in the History menu – accessed from gear icon at the top right in the “Analyze data” view) – once done, copy the link and paste it into the User > Histories “Import from file” button’s function. For Workflows, go to Workflows, click on the workflow’s menu and choose Share – on the next screen under Export, click on the Download button to generate a URL – paste that URL into the other server under Workflow > Import.
Notes: On some “from” servers, Datasets may need to be in a History in a “Shared by URL” state – and be sure to also check the box to share included datasets!. History archives always require the History (and included datasets) to be in a “Shared by URL” state (do this before generating the archive). Histories – the History may need to be in a “Shared by URL” state (another option in the History Menu) – be sure to also check the box to share included datasets!


Question 3: Can I personally move tools from one public Galaxy server to another?
Help 3: No but you can request that tools are installed at other servers. Or set up your own Galaxy and install any tools you want (since you’ll be the administrator!). The tools at any public Galaxy server are determined by the server administrators.
Notes: What is the tool not available at usegalaxy.eu? Include the full name/version from the top of the tool form. The tool may be no longer be supported, have an updated version, or be replaced. Or, maybe it has simply not been added yet. We can let you know and ask the usegalaxy.eu administrators if some tool install seems needed/possible – but no promises, they make the final decision.


There are other ways to transfer/move data between Galaxy servers or to download data as a backup. I’ve added a few more tags to your post with much more Q&A help that covers a broad range of use cases around this.

We also just added in new features that touch on these functions – so all of the above will go into a new FAQ after the next release and older FAQs will be updated. Tutorials may also be updated or added.

Best!

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