updated docker build to save time

PNNL-CompBio · Jul 8, 2024 · 91f8125 · 91f8125
1 parent df7702c
commit 91f8125
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Showing 3 changed files with 6 additions and 8 deletions.
diff --git a/build/broad_sanger/exp_requirements.r b/build/broad_sanger/exp_requirements.r
@@ -1,8 +1,9 @@
-install.packages("readr")
-install.packages("stringr")
-install.packages("dplyr")
+#install.packages("readr")
+#install.packages("stringr")
+#install.packages("dplyr")
 install.packages('reticulate')
-install.packages('tidyr')
+                                        #install.packages('tidyr')
+install.packages('tidyverse')
 install.packages("BiocManager")
 BiocManager::install("PharmacoGx",update=TRUE,ask=FALSE)
 
diff --git a/build/broad_sanger/omics_requirements.r b/build/broad_sanger/omics_requirements.r
@@ -5,5 +5,5 @@ install.packages("curl")
 install.packages("stringr")
 install.packages("dplyr")
 install.packages("XML")
-install.packages('reticulate')
+#install.packages('reticulate')
 install.packages('tidyr')
diff --git a/build/docker/Dockerfile.broad_sanger_exp b/build/docker/Dockerfile.broad_sanger_exp
@@ -1,14 +1,11 @@
 FROM r-base:4.2.1
 ENV DEBIAN_FRONTEND=noninteractive
 RUN apt-get update  --fix-missing
-#RUN apt-get install -y --fix-missing --allow-unauthenticated build-essential libpq-dev python3.10 python3-pip python3-setuptools python3-dev python3-venv libcurl4-openssl-dev libxml2-dev libglpk-dev
-
 RUN apt-get install -y --fix-missing --allow-unauthenticated build-essential python3-pip python3-setuptools python3-dev python3-venv libcurl4-openssl-dev libglpk-dev libxml2-dev libpq-dev
 
 RUN python3 -m venv /opt/venv
 RUN /opt/venv/bin/pip3 install --upgrade pip
 
-
 # Set MPLCONFIGDIR to a writable directory
 ENV MPLCONFIGDIR=/tmp/matplotlib
 RUN mkdir -p /tmp/matplotlib