- Create conda environment
- Install base R version 3.5
- Open R & Install dada2
- Install rstudio
- Final Notes
Getting dada2 installed on our new server
Create conda environment
I needed an older version of zlib for a future error with installing “ShortRead” which was solved thanks to this post This actually failed…. Instead trying to install ShortRead through bioconductor. Frankenstein time. I don’t know if this removes the speedup effect you get by natively installing dada2!! (Documented Below)
Install base R version 3.5
For some reason MRO was not working? But then a bunch of stuff wasn’t working. It is likely that MRO would be fine with this strategy, I just didn’t try after I finally got it working.
Fix the compiler issues with installing dada2 using Bioconductor (and not Anaconda). This was to try and avoid the 3-20x slowdown in dada2 that Ben Callahan documented here. This fix was provided from this post.
Install ShortRead through conda
Fix a resulting shared library issue (why?!)
Open R & Install dada2
Somehow this worked as well!
I really should have spent the time to figure out Rstudio Server and get that running. It would probably be smoothly than using this desktop version. However, we were on a time crunch and this seems to be keeping everyone happy for now!