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aryarm / varCA

Use an ensemble of variant callers to call variants from ATAC-seq data
MIT License
22 stars 7 forks source link

update dependencies and freeze them #10

Closed aryarm closed 4 years ago

aryarm commented 4 years ago

update them to their newest versions and then freeze them in the envs file (specifically, consider updating mlr)

this will decrease the chance of bugs arising in the future from new versions of the dependencies

aryarm commented 4 years ago

apparently data.table and mlr conflict in envs/classify.yml you should fix that

Update: they didn't conflict when I tried to install them on a different computer. maybe somebody else should try this?

aryarm commented 4 years ago

A note on mlr3: Updating from mlr2 to mlr3 would require rewriting a couple of our scripts, since the syntax has changed dramatically in mlr3 I don't think it would be too hard to do, but doing so wouldn't really seem to offer much of a benefit to us, especially since the move from mlr2 to mlr3 was primarily to change the syntax, as far as I can tell (source: https://mlr-org.com/docs/mlr3-0-1-0/) As a package, mlr just allows its users to execute a number of other packages in a standardized way. We use it to execute the ranger package, which contains the code for the random forest.

gmcvicker commented 4 years ago

If using mlr2 gives warnings to upgrade to mlr3 when the software is run, then i think we should probably go ahead and update the code. If switching is a lot of work, could we instead suppress the warning messages?