The answer I think depends largely on the kinds of changes you made and how quickly you need to deploy things. If the changes are bugfixes or enhancements in-line with the existing tool's structures - I think it would be best to open a pull request and try to get the tool fixed - the tophat2 tool for instance is hosted at https://github.com/galaxyproject/tools-devteam. If you are tweaking the environment for your tool (loading modules or something like that) - there are probably better things to do then modify the tool directly. Let me know what the change is and I may be able to help you figure out something we can do in job_conf.xml or with local Galaxy package dependencies. If you really just want a different interface to the same tool - you could consider creating a new repository for a ucdavis tophat tool. You should be able to reuse the same package_tophat, etc.... If they are really just local changes that you don't need/want to share - personally I would just manage them outside the tool shed. Create a folder within your tools directory or a whole separate repository just for your tools - and create say a local_tool_conf.xml file that links in all of those tools (e.g. https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/sampl...) and then make sure you configure your Galaxy instances to load this local_tool_conf.xml file. If you do this in a separate repository you shouldn't even need to fork repository. Create a local tool shed is also a solution - but I am not a fan of this. Hope this helps - I can be more specific if I have more information on the nature of the changes or how you would like to proceed. -John On Wed, Apr 15, 2015 at 7:56 PM, Nikhil Joshi <najoshi@ucdavis.edu> wrote:

Hi all,

So I am trying to push our toolshed directories to our own repo and I am running into problems. Basically, since the toolshed tools are subrepos, I can't figure out how to push those changes into *our* repo. Also, I have had to change some of the toolshed tools because they don't work properly with our galaxy. So, when I try to do the push, it aborts giving me this error:

abort: push creates new remote head b9bd905700fe! (in subrepo toolshed.g2.bx.psu.edu/repos/devteam/tophat2/da1f39fe14bc/tophat2)

And, of course, I can't push to that repo, nor do I want to. All I want to do is to push our shed tools directory to our repo, but at the same time keep the mercurial information so that when we clone our repo into a new galaxy install, the toolshed will still work from galaxy.

How can I do this? Am I even thinking about this the right way?

- Nik.

-- Nikhil Joshi Bioinformatics Analyst/Programmer UC Davis Bioinformatics Core http://bioinformatics.ucdavis.edu/ najoshi -at- ucdavis -dot- edu 530.752.2698 (w)

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