Hello Nir,

the tool publishing process looks like this: tools for Galaxy are contributed by developers like you to the Tool Shed https://toolshed.g2.bx.psu.edu/ which serves as an 'appstore' for Galaxies worldwide. Any Galaxy administrator can then instal the tool. Some tools have dependencies, yours seem to depend on R. The recommended way to have Galaxy installed these dependencies for you is to use Conda (list of some available R packages here: https://anaconda.org/r/repo?type=conda). To learn more about Conda please visit https://docs.galaxyproject.org/en/master/admin/conda_faq.html

Alternatively, when you do not care about sharing your tool, and you do not need to track reproducibility you can add any tool to Galaxy locally (add the .xml wrapper and point tool_conf.xml at it and restart Galaxy). When the tool is executed and no dependencies are found Galaxy will look for its executable and if it is on the $PATH it will just use it.

Please let us know if you have more questions.

Thanks for using Galaxy,

Martin

On Thu, Feb 9, 2017 at 11:01 AM Nir Shachaf nir.shachaf@weizmann.ac.il wrote:

Dear Galaxy-dev team,

As a research scientist in the dept. of Plant Sciences I would like to contribute a tool to the 'Metabolomics' tool-box under Galaxy. The tool is principally written in R, with some dependencies (namely: R>=3.x, and several R packages). Following the documentation in:

https://wiki.galaxyproject.org/Admin/Tools/ToolDependencies

https://wiki.galaxyproject.org/Admin/Config/ToolDependencies

I admit I get confused by the numerous possibilities offered by the framework. My main concern is to be able to link the Galaxy server to tools already installed on my development environment, and NOT to depend on the tools available in the tool-shed repository (as many are not there, and there are specific versions requirements).

Could you kindly direct me to the relevant solution, or a user's-list post, if applicable?

Many thanks in advance, Nir Shachaf, Plant Sciences Dept., Weizmann Inst. of Science, Rehovot, Israel. ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/

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