From 86dd7cf0bf2637d94c844f7a123b1dd442c5b213 Mon Sep 17 00:00:00 2001
From: Andrea Dell'Amico <andrea.dellamico@isti.cnr.it>
Date: Mon, 10 Apr 2023 17:19:23 +0200
Subject: [PATCH] Install python3 and other dependencies

---
 Dockerfile | 15 +++++++++++----
 1 file changed, 11 insertions(+), 4 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index d7091bb..c7802e3 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -6,8 +6,13 @@ LABEL org.d4science.image.licenses="EUPL-1.2" \
       org.d4science.image.authors="Andrea Dell'Amico <andrea.dellamico@isti.cnr.it>"
 
 ENV DEBIAN_FRONTEND noninteractive
-# Some R dependencies
-RUN apt-get update && apt-get install -y \
+# Upgrade, install some R dependencies and base python3
+RUN apt-get update --yes && \
+    apt-get dist-upgrade --yes && \
+    apt-get install --yes --no-install-recommends \
+    python3 \
+    python3-pip \
+    curl \
     jags \
     libxml2 \
     git \
@@ -16,6 +21,8 @@ RUN apt-get update && apt-get install -y \
     libsodium-dev \
     libudunits2-dev \
     libfontconfig1-dev \
+    librdf0 \
+    librdf0-dev \
     netcdf-bin \
     libcairo2-dev \
     libharfbuzz-dev \
@@ -57,8 +64,7 @@ RUN for cr in `cat /tmp/jupyter-image-r-cran-pkgs.txt` ; do \
 
 # From github
 ADD https://code-repo.d4science.org/gCubeSystem/r-packages-list/raw/branch/master/r_github_pkgs.txt /tmp
-RUN mkdir -p /etc/R
-RUN echo "GITHUB_PAT=$GITHUB_PAT" >> /etc/R/Renviron.site
+RUN echo "GITHUB_PAT=$GITHUB_PAT" >> /usr/local/lib/R/etc/Renviron.site
 #RUN for g in `cat /tmp/r_github_pkgs.txt` ; do \
 #    Rscript --slave --no-site-file --no-init-file --no-save --no-restore-history \
 #    -e " require(devtools); devtools::install_github('$g')" ; done
@@ -69,6 +75,7 @@ RUN installGithub.r -d TRUE -u FALSE -r https://packagemanager.rstudio.com/all/_
 RUN installGithub.r -d TRUE -u FALSE -r https://packagemanager.rstudio.com/all/__linux__/focal/latest sofia-tsaf/SOFIA
 RUN installGithub.r -d TRUE -u FALSE -r https://packagemanager.rstudio.com/all/__linux__/focal/latest jabbamodel/JABBA
 RUN installGithub.r -d TRUE -u FALSE -r https://packagemanager.rstudio.com/all/__linux__/focal/latest tokami/lbmsmt
+RUN installGithub.r -d TRUE -u FALSE -r https://packagemanager.rstudio.com/all/__linux__/focal/latest james-thorson/FishLife
 
 # Ensure that we remove the source packages
 RUN rm -fr /tmp/downloaded_packages/*