Merge pull request #57 from nmfs-opensci/eeholmes-patch-1

Update appendix

Author: eeholmes

appendix

@@ -8,8 +8,10 @@ RUN PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin && \
   ${REPO_DIR}/rocker.sh
 
 # Install extra cmd line packages after R installation
-RUN apt-get update && \
-  xargs -a ${REPO_DIR}/apt-extras.txt apt-get install --yes --no-install-recommends && \
+# The package_list part is reading the file and doing clean-up to just have the list of packages
+RUN package_list=$(grep -v '^\s*#' ${REPO_DIR}/apt-extras.txt | grep -v '^\s*$' | sed 's/\r//g; s/#.*//; s/^[[:space:]]*//; s/[[:space:]]*$//' | awk '{$1=$1};1')
+  apt-get update && \
+  apt-get install --yes --no-install-recommends $package_list && \
   apt-get autoremove --purge && \
   apt-get clean && \
   rm -rf /var/lib/apt/lists/*