Jim; Thanks for the interest in the nglims code. This currently needs some work to get back working cleanly with the latest versions of Galaxy since the Javascript libraries changed and jWizard seems unhappy with the latest jQuery.

So the current status is still, try it out since it needs some work and please don't replace your production Galaxy with it. Apologies that we haven't had much time to work on it. I was hoping to try and think of ways to reboot this as a community project that integrates more cleanly with Galaxy updates this summer at the conference. There is also a Galaxy lims from Jelle Scholtalbers:

https://www.ncbi.nlm.nih.gov/pubmed/23479349 https://bitbucket.org/jelle/galaxy-central-tron-lims/

That might be worth looking at as well.

You should be able to put the tools from a bcbio-nextgen installation into the $PATH for use via Galaxy. The genomes also use standard Galaxy *.loc files, so you just need to ensure your Galaxy instance points to them and it can use the same genomes.

Hope this helps some, Brad

Brad,

We are looking for some advice on going from our current Galaxy to the nglims fork of Galaxy you have created. The last post I've seen on the subject of moving to the nglims Galaxy was here: http://user.list.galaxyproject.org/add-nglims-to-galaxy-dist-td4656015.html

Is it still the case that it "would best to first try it out on a separate instance before thinking about integrating with your production Galaxy. It does take a bit of tweaking …." ??

Second, when I install the nglims fork of galaxy is there a way to have galaxy use the tools and genomes in bc-bio? On our original install, before we used bc-bio, I added tools mainly via the tool shed. It would be nice be to have galaxy using the same tools.

Any other advice would be greatly appreciated.

Thanks Jim --

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