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/samples_tool_conf.xml) 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 <najo...@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) > > ___________________________________________________________ > 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/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ ___________________________________________________________ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
