Merge pull request #128 from toniher/devtools-fix

Devtools fix for Docker build problem

Dockerfile

@@ -1,13 +1,14 @@
-FROM rocker/r-ver:3.6.3
+FROM rocker/tidyverse:3.6.3
 
-# File Author / Maintainer
-MAINTAINER Toni Hermoso Pulido <[email protected]>
+LABEL maintainer="Toni Hermoso Pulido <[email protected]>"
 
 ARG BOWTIE_VERSION=1.2.1.1
+ARG GETOPT_VERSION=1.20.3
+ARG OPTPARSE_VERSION=1.7.3
 ARG PSIPLOT_VERSION=2.3.0
 
 # Install external dependencies 
-RUN apt-get update -qq && apt-get upgrade -y && apt-get install -y --no-install-recommends python curl libcurl4-openssl-dev libssl-dev libsqlite3-dev libxml2-dev qpdf git
+RUN apt-get update --allow-releaseinfo-change && apt-get upgrade -y && apt-get install -y --no-install-recommends python curl libcurl4-openssl-dev libssl-dev libsqlite3-dev libxml2-dev qpdf git
 RUN apt-get install -y build-essential libharfbuzz-dev libfontconfig1-dev libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev libfribidi-dev
 
 # Install bowtie 
@@ -19,14 +20,18 @@ RUN cd /usr/local; rm bowtie-${BOWTIE_VERSION}-linux-x86_64.zip
 # Let's put in PATH
 RUN cd /usr/local/bin; ln -s ../bowtie-${BOWTIE_VERSION}/bowtie* .
 
-COPY deps.R /usr/local
+# Not used anymore
+# COPY deps.R /usr/local
+# RUN Rscript /usr/local/deps.R > /tmp/deps.log
 
-RUN Rscript /usr/local/deps.R > /tmp/deps.log
-
-# Psiplot
+# Github packages
+RUN cd /usr/local/; curl --fail --silent --show-error --location --remote-name https://github.com/trevorld/r-getopt/archive/v${GETOPT_VERSION}.tar.gz
+RUN cd /usr/local/; curl --fail --silent --show-error --location --remote-name https://github.com/trevorld/r-optparse/archive/v${OPTPARSE_VERSION}.tar.gz
 RUN cd /usr/local/; curl --fail --silent --show-error --location --remote-name https://github.com/kcha/psiplot/archive/v${PSIPLOT_VERSION}.tar.gz
+RUN Rscript -e "install.packages( \"/usr/local/v${GETOPT_VERSION}.tar.gz\", repos = NULL )"
+RUN Rscript -e "install.packages( \"/usr/local/v${OPTPARSE_VERSION}.tar.gz\", repos = NULL )"
 RUN Rscript -e "install.packages( \"/usr/local/v${PSIPLOT_VERSION}.tar.gz\", repos = NULL )"
-RUN rm /usr/local/v${PSIPLOT_VERSION}.tar.gz
+RUN rm /usr/local/v${PSIPLOT_VERSION}.tar.gz; rm /usr/local/v${OPTPARSE_VERSION}.tar.gz; rm /usr/local/v${GETOPT_VERSION}.tar.gz
 
 # Install Vast-tools
 RUN mkdir -p /usr/local/vast-tools