Question: List of tools integrating with Galaxy (like BioMart, GO or Refinery) ?
0
gravatar for Biosok
7 weeks ago by
Biosok10
UK
Biosok10 wrote:

Hey all,

I recently started a project that uses a Galaxy instance to run a number of workflows and I want to look into expanding its resources/uses. For that reason I am looking for tools that integrate with Galaxy (like BioMart, GO, Refinery). Is there a list of such resources available somewhere and if not, could anyone suggest some of those tools? Thanks a lot in advance!

Kind Regards

general intergration tools • 79 views
ADD COMMENTlink modified 7 weeks ago by Jennifer Hillman Jackson23k • written 7 weeks ago by Biosok10
1
gravatar for Jennifer Hillman Jackson
7 weeks ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello,

Tools under "Get Data" at https://usegalaxy.org are a starting place.

Others can be found by searching in the tool panel - some use indexed files, but others work directly with external sources. Examples: NCBI SRA Tools, SnpEff available databases/Download.

For others available in the wider community, you can look in the Tool Shed (http://usegalaxy.org/toolshed).

I do not know of a comprehensive, curated list of external sites that all tools directly interact with. This could be a useful resource, but the downside is that it could get outdated quickly as new tools are created and older tools deprecated (and might be why such a list does not exist already). Tools are developed by the wider community and do not require review to be published in the Tool Shed. They must simply meet the technical requirements of an intact repository. This is by design to allow open-source publishing without excessive hurdles.

In general, the more downloads, the more successful/popular the tool is, which is a type of community vetting. And if a tool is found on a public server, it was almost certainly reviewed by the server owners for quality/usability. Some groups that publish tools have published coding standards and other guidelines (standard ways of designing tool tests, help sections, form design, and the like), but that does not by any means indicate that tools contributed by individuals independently are not as "good". A repository that is marked as "valid" does indicate that a tool includes all of the basic components, including tool tests, complete descriptions, and other extras (meaning, these components are present, not that they have been through some sort of overarching QA approval process).

All that said, if you wanted to share what you find/generate, you could consider adding that to http://galaxyproject.org as a new FAQ. Perhaps in the Admin area, although I can think of a few other places it would fit. It could be given a "last updated" note (in markdown, so is visible on the page to readers) along with notes about how the list was generated to allow others to also contribute to the FAQ ongoing. All are welcome to contribute to this site. Open a pull-request with the content and our team will review and give feedback (or accept it as-is if well written/organized and fits in with related content).

Good question! Jen, Galaxy team

ADD COMMENTlink modified 7 weeks ago • written 7 weeks ago by Jennifer Hillman Jackson23k
1

Hi Jen,

Thanks for the detailed and timely reply, I really appreciate it. Indeed I couldn't find any sort of tool list populated by the wider community. In my case, the lab is exploring the galaxy tools that can be interesting and are not included in the standard toolshed (as we already looked into that). Since you mentioned that there is not an overarching QA approval procedure I must be very careful while "accepting" independent tools (probably by taking into account downloads, how public the server is etc.). I would be happy to contribute my findings as you see fit.

Regards! Sokratis

ADD REPLYlink written 7 weeks ago by Biosok10
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