New wrapped tool request for the IUC or Finding existing wrapped tools. Example: genome scaffolder

Can I request Genome scaffolder on galaxy?

1 Like

Hello @Rahul_Shelke

New wrapped tool requests can be made to the IUC by creating a ticket here: https://github.com/galaxyproject/tools-iuc/

Or, you can vet the request first at their Gitter channel here. Someone may already be working on wrapping this tool, or a related tool: https://gitter.im/galaxy-iuc/iuc

Existing wrapped tools can be searched for at the ToolShed https://usegalaxy.org. You can check to see which servers have any of these tools installed already by reviewing/searching the tool panel of that server (keyword: “assembly” will almost always work best).

Thanks!

Hi Jennifer,
These tools are available on some galaxies, but they are not working properly. I shared the error with admins but not got any reply from them.

Regards

rahul

1 Like

@Rahul_Shelke

What is the full tool name, including version? I didn’t find it in the Main ToolShed https://usegalaxy.org/toolshed and some public Galaxy servers will write/host custom tools and not publish them there.

But we can double-check that I didn’t miss it.

  1. What public Galaxy servers is the tool available at? URLs please
  2. What is the full tool name as shown in the user interface when the tool is brought up? This is the entire name, including version, at the very top of the tool form.
  3. What is the “Galaxy Tool ID:” and “Galaxy Tool Version:” (might need to look for it that way). Click on the “i” view details icon for an error dataset the tool produced. On that page, under the section “Job Information”, you’ll find two lines for that info listed first. Post those complete report lines back here. Don’t share the rest of the report (some of it would expose private info).

We might be able to help you to make contact with either the tool author or the servers hosting the tool, might not, but it is worth a try.

Dear Jennifer,

                    Following are the name of tools available in the Main ToolShed https://usegalaxy.org/toolshed  (Assembly section).
  1. Abyss 2. Sspace 3. Sopra

Moreover,

Abyss also available on

  1. http://biomaster.atica.um.es:8080/

  2. https://orione.crs4.it/

Sopra,

  1. https://usegalaxy.eu/

  2. https://orione.crs4.it/

Sspace,

  1. https://orione.crs4.it/

  2. https://toolshed.g2.bx.psu.edu/repository/display_tool?repository_id=260b50f4434ddc87&render_repository_actions_for=tool_shed&tool_config=database%2Fcommunity_files%2F000%2Frepo_589%2Fsspace.xml&changeset_revision=b3a6b51c44e0

  3. https://mississippi.snv.jussieu.fr/

Soapdenovo

  1. http://gigagalaxy.net/
1 Like

Right – not all tools are available on all servers. This is usually because of the particular resources different public servers have.

These tools all fail, at all of the servers you listed? Or, these are not the tool you want to use? I’ve lost track of what you are asking for.

Dear Jennifer,
Following are the issues associated with running listed tools on other public galaxies .

  1. These tools are not maintained.

  2. Not enough space on that galaxies.

  3. Job are running for month but not getting finished.

  4. No option of error report sharing. Etc

Due to these all collective issues jobs are not running smoothly. When I contacted admin, they reuested me to use main galaxy and directed me to request for listed tools.

Coming to earlier mail I had requested you to provide Abyss, Sopra, Sspace tools on galaxy main. Abyss is maintained by IUC? Is it not possible to add abyss assembler in main galaxy? Not a single scaffolder is available on main galaxy.

Regards

Rahul

1 Like

@Rahul_Shelke

Thanks for explaining. All of these tools require significant computational resources. Too much for the usegalaxy.* public Galaxy servers (why we do not host them) and it sounds like in your case, too much for the other public servers you tried as well. The exception, Sopra, hosted at the usegalaxy.eu server might be able to handle some assemblies and not others (based on content/volume). Even they do not host Abyss on that server and the admins are part of the IUC.

There are many other ways to use Galaxy. Setting up a cloud Galaxy server is a popular option when working with very large data and/or tools that require significant computational resources (fail at public servers, or are not hosted at all). A local Galaxy server will require more administrative configuration plus access to storage/compute resources that are sufficient to process the data. The resources a Galaxy wrapped 3rd party tool requires is about the same as when running that same tool line-command.

Please see:

Hope that helps to explain! I’m not sure why the other admins asked to have the tool(s) added to usegalaxy.org, maybe they thought we had the resources, or that it was at least worth checking. But, the solution for you is almost certainly a scaled-up cloud Galaxy server.