How do I go about submitting a patch to the project? I added support for quartile normalization to cufflinks and cuffdiff and I'll add the option to include replicates with cuffdiff next.

That's good news Rory. You can submit patches one of two ways:

(1) Set up a fork/patchqueue of Galaxy in bitbucket and send links to major changesets/patches;

(2) Send the patch file. You can create a patch file of your changes from the galaxy-central directory as follows:

% hg diff > my_patch_name.patch

For larger and/or ongoing patches, (1) is highly preferred to (2). Please submit all patches to galaxy-dev@bx.psu.edu (cc'd), which is the mailing list for local community development and installation. You may also find the list useful for discussing questions or ideas you may have.

Thanks,