Methylation Tool Setup

Install the methylation tool into a new galaxy instance:

Upload the tool from the custom toolshed and install the conda env through the Galaxy UI. In the terminal, activate the new conda env, while impersonating the user with full galaxy access. Within the conda env, activate R and run the following commands:

install.packages(c("randomForest","glmnet","ggplot2","gridExtra","knitr","Rtsne","pander","plotly"))

and

if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install(c("lumi","methylumi","conumee","minfi","IlluminaHumanMethylation450kmanifest","IlluminaHumanMethylationEPICmanifest"))

They may throw errors at you, but most likely these errors can be ignored. Known ignorable errors include:

installation of package ‘’ had non-zero exit status

Error in setwd(od) : cannot change working directory Error in setwd(startdir) : cannot change working directory Execution halted

Once both commands have finished exit R and save the workspace image. "q(y)"

Back in the Galaxy UI run the tool using the option "Setup Install?" -> YES

If this finished without error you should be good to go but, to be certain, run it again with "Setup Install?" -> NO

If this also works you are definitely good to go.