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.
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.
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
> 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
> najoshi -at- ucdavis -dot- edu
> 530.752.2698 (w)
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