- The Picard version used (1.139) is quite old. Would be nice to be able to use the current 2.9.0 version. (Natasha will test)
- ~~The two SPP scripts (`run_spp.R` and `run_spp_nodups.R`) need to be packaged up in Conda in a sane way. (Adam will do)~~ **Done now, `phantompeakqualtools` created.**
- ~~The two SPP scripts (`run_spp.R` and `run_spp_nodups.R`) need to be packaged up in Conda in a sane way. (Adam will do)~~ **Done now, `phantompeakqualtools` package created.**
- How to distribute the MongoDB stuff in a sane way. Docker is currently the leading candidate. The size of the experiments and samples collection is a little over 1GB, which isn't terribly large. We could create a container with Mongo installed and the DB pre-populated, and then include scripts to do the update from ENCODE.
