Question: Custom toolshed linked with Galaxy toolshed
gravatar for danielsauceda
16 months ago by
Texas A&M
danielsauceda60 wrote:

So here is the situation. I am hosting a toolshed via apache proxypass etc. It works fine. I am proceeding to create tools for data processing and uploading them into my "custom toolshed" for my particular set of users. however there are a number of tools from the Main Toolshed that I like but most of them I will never need.

Ideally I would like my users not see the Main Toolshed and only have access to my select tools hosted in my custom toolshed.

Is there a way of linking or back-ending select Main Toolshed tools into a custom toolshed such that proper credit is given and updates are received? (Without manually loading each one up)

ADD COMMENTlink modified 15 months ago by Jennifer Hillman Jackson25k • written 16 months ago by danielsauceda60
gravatar for Jennifer Hillman Jackson
15 months ago by
United States
Jennifer Hillman Jackson25k wrote:


General users will only see the tools in the tool panel when using Galaxy. If there are installed tools from the MTS that you do not want users to see/use, these can be "hidden" in the tool panel.

Only admins will ever see the Tool Shed - it is not accessible to general users through the Galaxy UI (to install tools, etc). The exception is link-out under "Options > See in Tool Shed" when a tool is active in the center panel. This redirects to where the tool was sourced. I suppose this could be edited if needed.

You may have other reasons for wanting to mirror the Main Tool Shed. The process would be the same as mirroring any other server/content. We don't have a special procedure developed and I am not aware of one developed and/or running in the community. The purpose of the MTS is to be a shared community resource - for contribution and distribution of Galaxy wrapped tools.

And there isn't a way to send data back - by "credit" do you mean feedback on the number of installs? There is a convenience statistic in the MTS for how many times a tool has been installed to give admins some idea about how often a tool has been used/vetted by the community, but that is the only purpose. Missing your installs would not change the values much - and tools (from devteam, IUC, others) that can be directly installed (even if in the MTS) already have no install counts recorded.

If by "credit" you instead mean how to cite: Some tools may have notes about how to cite them or you can just capture the tool wrapper details and cite that. Galaxy itself should be cited if used in a publication.

If your question was misunderstood, please clarify more.

Thanks, Jen, Galaxy team

ADD COMMENTlink written 15 months ago by Jennifer Hillman Jackson25k

And there isn't a way to send data back - by "credit" do you mean feedback on the number of installs?

Yes that is what I meant. But the citation specification in the tool is probably more important and I will use that.

This is more for single user cases where a person clones and runs Galaxy locally. However, Rather than adding tools from MTS, they would use my Custom TS (CTS) that I am hosting. But I would like to take some tools (discipline independent) from MTS and put them in CTS. So it would be like "Selective Mirroring of MTS.

Although I am Linux savvy, webDev is not: "The process would be the same as mirroring any other server/content" is unfamiliar to me and Would not mind attempting to Mirror it. But If you know of any links or webpages (galaxyproject or not) as a starting place it would be much appreciated.

Daniel Sauceda

ADD REPLYlink written 15 months ago by danielsauceda60

Thanks for additional info.

Instead of a full mirror, using the Tool Shed API to pull what you need is probably a better solution. A script that runs at certain intervals could check for updates and the like.

An alternative is to create a Docker (or Cloudman) Galaxy that has the MTS tools installed when launched, then your custom TS is accessed from that point forward to add more. Or, include all, creating a "Galaxy server flavor" that suits your researchers. Even reference data can be included - this is commonly done for teaching pre-configured Galaxies.

Galaxy Docker/Cloudman and API help is in a few places, start here:

Also please see "Education" at the Galaxy Hub for how others are customizing and deploying pre-configured Galaxy instances (not frozen, just pre-configured at a baseline).

ADD REPLYlink written 15 months ago by Jennifer Hillman Jackson25k
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