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- The Picard version used (1.139) is quite old. Would be nice to be able to use the current 2.9.0 version.
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- The two SPP scripts (`run_spp.R` and `run_spp_nodups.R`) need to be packaged up in Conda in a sane way.
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- 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. |