diff --git a/build/broad_sanger/exp_requirements.r b/build/broad_sanger/exp_requirements.r index 2e4c2275..9cc16e17 100755 --- 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 index 98a4be32..785dc09a 100755 --- 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 index 7a8207f9..1b1b1600 100755 --- 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