Merge branch 'feature/cleanup-and-refactor'

Dockerfile

@@ -1,6 +1,9 @@
-FROM sneumann/metfamily-base:latest
+#FROM sneumann/metfamily-base:latest
+FROM sneumann/metfamily-base:4.3.2
+#FROM sneumann/metfamily-base:4.0.5
+#FROM sneumann/metfamily-base:3.6.3
 
-MAINTAINER Kristian Peters <kpeters@ipb-halle.de>
+MAINTAINER Steffen Neumann <sneumann@ipb-halle.de>
 
 LABEL Description="MetFamily helps identifying metabolites and groups them into metabolite clusters (a.k.a. families)."
 

Dockerfile-base

@@ -1,30 +1,35 @@
 # syntax=docker/dockerfile:1.3-labs
-FROM rocker/shiny:3.6.3
+FROM rocker/shiny:4.3.2
 
-MAINTAINER Kristian Peters <kpeters@ipb-halle.de>
+MAINTAINER Steffen Neumann <sneumann@ipb-halle.de>
 
 LABEL Description="MetFamily Base Image with dependencies."
 
+## Older base images might need libigraph0-dev instead of libigraph-dev 
 RUN apt-get -y --allow-releaseinfo-change update && apt-get -y install \
-  netcdf-bin libnetcdf-dev libdigest-sha-perl libigraph0-dev \
+  netcdf-bin libnetcdf-dev libdigest-sha-perl libigraph-dev \
   xorg-dev libglu1-mesa-dev freeglut3-dev libgomp1 libxml2-dev gcc g++ libcurl4-gnutls-dev libssl-dev gdebi-core libharfbuzz-dev libfribidi-dev libtiff5-dev
 
 ENV NETCDF_INCLUDE=/usr/include
 RUN echo 'sanitize_errors off;disable_protocols xdr-streaming xhr-streaming iframe-eventsource iframe-htmlfile;' >> /etc/shiny-server/shiny-server.conf
 
-COPY <<EOF /root/.Rprofile
-local({
-  r <- getOption(\"repos\")
-  r[\"CRAN\"] <- \"https://packagemanager.posit.co/cran/2020-04-23/\"
-  options(repos=r)
-})
-EOF
+## The following Rprofile allows to use CRAN snapshots
+## (The HERE document COPY <<EOF requires syntax=docker/dockerfile:1.3-labs)
+## We have tested the following combinations of FROM and CRAN:
+## rocker/shiny:3.6.3	https://packagemanager.posit.co/cran/2020-04-23/
+## rocker/shiny:4.0.5	https://packagemanager.posit.co/cran/2021-03-01/
+## rocker/shiny:4.3.2	https://packagemanager.posit.co/cran/2023-12-01/
+
+## COPY <<EOF /root/.Rprofile
+## local({
+##   r <- getOption(\"repos\")
+##   r[\"CRAN\"] <- \"https://packagemanager.posit.co/cran/2021-03-01/\"
+##   options(repos=r)
+## })
+## EOF
 
 ADD DESCRIPTION /tmp/MetFamily/DESCRIPTION
 RUN R -e 'options(warn=2) ; install.packages("devtools")'
-RUN R -e 'options(warn=2) ; install.packages("XML")'
-RUN R -e 'options(warn=2) ; install.packages("MALDIquant")'
-RUN R -e 'options(warn=2) ; install.packages("FactoMineR")'
 RUN R -e 'library(devtools); options(warn=2) ; install_deps("/tmp/MetFamily")'
 
 WORKDIR /srv/shiny-server