Merge pull request #208 from Sage-Bionetworks/fix-docker-r-install

Install bioconductor packages correctly
Sage-Bionetworks · Oct 4, 2019 · 301f907 · 301f907
2 parents db956bc + 27025db
commit 301f907
Showing 1 changed file with 5 additions and 4 deletions.
diff --git a/docker/installPackages.R b/docker/installPackages.R
@@ -5,12 +5,13 @@ install.packages("rmarkdown", repo="https://ftp.osuosl.org/pub/cran/")
 install.packages("UpSetR", repo="https://ftp.osuosl.org/pub/cran/")
 install.packages("testthat", repo="https://ftp.osuosl.org/pub/cran/")
 
-source("https://bioconductor.org/biocLite.R")
-biocLite("VariantAnnotation")
+install.packages("BiocManager", repo="https://ftp.osuosl.org/pub/cran/")
+BiocManager::install("VariantAnnotation")
 
 library(synapser)
 library(dplyr)
 library(argparse)
 library(UpSetR)
-library(VariantAnnotation)
-library(testthat)
+library(rmarkdown)
+library(testthat)
+library(VariantAnnotation)