What plugin or other thing could I best use as a skeleton or template?


#1

I’m still debating about installing qiime2 and using it to test some experimental
code. The c++ code currently reads and indexes a fasta containing known
sequences and another fasta or stream containing unknowns to score against the knowns. I’d like to compare the scores to related algorithms.
This sounds like something qiime2 can do in various ways. Is there
a particular module or plugin I could just about copy except have
it point to my code? Ideally it would use native code as I have
not done much with python and could copy the existing interface. Would a minimal test implementation
run ok with 1Gb of total disk usage ( installation files and any temp files )
and similar amount of RAM? Right now the code has thread safe
pthreads input stream reader and can use multiple cores but is ok without
all of that. Currently it obtains configuration info from command line params, a config file, and an interactive console mode using readline. For debugging I typically
use the console interactive mode except for maybe gdb when it segfaults reliably lol.

Thanks.


(Nicholas Bokulich) #2

(Matthew Ryan Dillon) #3

(Matthew Ryan Dillon) #4

(Matthew Ryan Dillon) #5

I agree!

I would suggest looking at building a plugin, or, a new method in an existing plugin.

Check out @cduvallet’s excellent blog post about getting started with plugin dev. Once you look at that, I would recommend spending some time on the QIIME 2 Developer Docs. If you get stuck or have any questions, you know where to find us.

QIIME 2 doesn’t know anything about bioinformatics until you teach it (through a plugin) - most of the overhead requirements will be driven by your plugin.

Hope that helps. :t_rex:


(Matthew Ryan Dillon) #6