...

scripts/container.def

 Bootstrap: docker
 
-From: ubuntu:18.04
+From: rocker/verse:3.6.2
+
+%files
+    install.R /tmp/install.R
 
 %post
     # non-interactive debconf
@@ -22,11 +25,12 @@ From: ubuntu:18.04
     pip3 install snakemake
 
     # install bcftools
+    export BCFVER=1.10.2
     apt-get -y install \
         gcc wget make zlib1g zlib1g-dev libbz2-dev liblzma-dev libcurl4-openssl-dev
-    wget https://github.com/samtools/bcftools/releases/download/1.9/bcftools-1.9.tar.bz2
-    tar -xvjf bcftools-1.9.tar.bz2
-    cd bcftools-1.9
+    wget https://github.com/samtools/bcftools/releases/download/1.9/bcftools-$BCFVER.tar.bz2
+    tar -xvjf bcftools-$BCFVER.tar.bz2
+    cd bcftools-$BCFVER
     ./configure --prefix=/usr/bcftools
     make
     make install
@@ -42,22 +46,11 @@ From: ubuntu:18.04
 
     # download, extract and store (brain) weights
     mkdir /usr/predixcan
-    wget https://s3.amazonaws.com/predictdb2/GTEx-V7_HapMap-2017-11-29.tar.gz -O /usr/predixcan/GTEx-V7_HapMap-2017-11-29.tar.gz
-    (cd /usr/predixcan; \
-        mkdir GTEx-V7_HapMap-2017-11-29; \
-        # we only need the brain tissue weights:
-        tar -xvz -f GTEx-V7_HapMap-2017-11-29.tar.gz -C GTEx-V7_HapMap-2017-11-29 --wildcards "*_Brain_*"; \
-        rm GTEx-V7_HapMap-2017-11-29.tar.gz \
-        )
+    wget https://zenodo.org/record/3518299/files/mashr_eqtl.tar?download=1 -O /usr/predixcan/mashr_eqtl.tar.gz
 
     # predixcan connects to the weights database with sql, needs write permission
     # even if the file system will be read only for the container
     chmod -R 777 /usr/predixcan
 
-    # install R and packages
-    apt-get -y install r-base
-    Rscript -e "install.packages('dplyr')"
-    Rscript -e "install.packages('yaml')"
-    Rscript -e "install.packages('purrr')"
-    Rscript -e "install.packages('readr')"
-    Rscript -e "install.packages('tidyr')"
+    # install R packages
+    Rscript /tmp/install.R

scripts/install.R

+options(
+    repos = list(
+        "https://mran.revolutionanalytics.com/snapshot/2020-03-01/"
+    )
+)
+
+install.packages("tidyverse")
+install.packages("pander")