As I adapt Galaxy to the needs of the particular workflows I'm
implementing, I invariably end up "tweaking" the existing code,
especially the tool definitions and the datatypes config file. These
tweaks are often minor - e.g. adding an extra parameter to Ross Lazarus'
ClustalW's code, changing the way the binary is called (e.g. clustalw2
on ubuntu is installed as clustalw, BLAST+ is installed single threaded
so the -num_threads option in the ncbi_blastn_wrapper.xml doesn't work),
a) Sometimes they make sense to share with the rest of the Galaxy community
b) local changes make it more tricky to keep in sync with upstream
changes to Galaxy
What's the best procedure for proposing changes up upstream galaxy?
Posting patches to galaxy-dev? Is there some mercurial magic that can help?
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