Hi, I want to run Pindel on galaxy but it doesn’t seem to pre-exist in the tools. Is there a way to add it in?
Thanks!
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A good intro to how tools work (and are made) can be read here: https://galaxyproject.org/tools/
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@Athina In addition to what @marten states, there is a wrapped version of this tool and a related tool already in the ToolShed Galaxy | Tool Shed. Search with the keyword “pindel” to find them.
These could be installed into your own local/cloud Galaxy and allocated sufficient resources. The resourced need to run any tool as wrapped for Galaxy is the same as needed when running the tool line-command, so the underlying tool’s manual can be referred to.
Small warning – the tools were last updated in 2016. If you decide to go this route and give them a try, and there are tool to install problems or errors when using them, report the problems to the tool author at their Github repository as an issue. The Github repo is linked on both of these tool’s pages in the ToolShed.The tool’s repositories have smaller example data – be sure to try that, not just your own data, to make sure the problem is tool related and not data/input related.
The same tool authors also host a public Galaxy server: https://mississippi.snv.jussieu.fr/. However, they only have one of the tools hosted (and not the primary tool). Probably because the jobs are computationally expensive, but you could ask them about it. Contact information is usually on the home page of public servers and/or here: Galaxy Platform Directory: Servers, Clouds, and Deployable Resources - Galaxy Community Hub. This server’s page is here (with a contact email): MISSISSIPPI - Galaxy Community Hub
I hope that combined this gives you some options!
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@jennaj Thank you! I will give it a go
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@jennaj Hello, I have added Pindel in my local Galaxy but now gives me a “Fatal Error: Exit code 127 ()”. I noticed as you mentioned that it has moved (as you mentioned) to Mississippi2 but not the main tool. However, I don’t see why it doesn’t work on my local Galaxy since I directly downloaded it from the tool shed? Could you please help?