Develop

jupyter-eiaspatial-notebook/jammy/Dockerfile

@@ -38,8 +38,8 @@ RUN echo "deb http://security.ubuntu.com/ubuntu focal-security main" | sudo tee
     sudo apt-get install libssl1.1 -y
 
 RUN cd /tmp && \
-    wget https://download2.rstudio.org/server/focal/amd64/rstudio-server-2023.09.0-463-amd64.deb && \
-    sudo gdebi -n rstudio-server-2023.09.0-463-amd64.deb
+    wget https://download2.rstudio.org/server/focal/amd64/rstudio-server-2024.09.0-375-amd64.deb && \
+    sudo gdebi -n rstudio-server-2024.09.0-375-amd64.deb
 
 ENV PATH=$PATH:/usr/lib/rstudio-server/bin
 
@@ -91,13 +91,10 @@ RUN cp -r /opt/DSSAT/v4.8.1.40/dssat-csm-data/* /opt/DSSAT/v4.8.1.40
 RUN sed -i 's,/usr/local,opt/DSSAT/v4.8.1.40,g' /opt/DSSAT/v4.8.1.40/DSSATPRO.L48
 RUN chown -R jovyan:users /opt/DSSAT/v4.8.1.40/*
 
-## ApsimX
-RUN sudo apt-get update && sudo apt-get install libsqlite3-dev dotnet-sdk-6.0 -y
-
-RUN cd /opt/ && \
-    sudo git clone https://github.com/APSIMInitiative/ApsimX && \
-    sudo chown -R jovyan:users /opt/ApsimX/. && \
-    sudo dotnet build -c Release ./ApsimX/ApsimX.sln
+# ApsimX
+RUN sudo apt-get update && sudo apt-get install libsqlite3-dev dotnet-sdk-6.0 gtk-sharp3 libgtksourceview-4-0 zenity -y
+COPY ./apsim-7592.deb ./apsim-7592.deb
+RUN sudo dpkg -i apsim-7592.deb
 
 ### Jupyter extensions & plugins installation
 RUN pip install aquirdturtle_collapsible_headings
@@ -124,7 +121,7 @@ RUN sudo Rscript packages.R
 ### Python packages installation
 RUN conda install -c conda-forge --file requirements.txt -y
 
-RUN rm packages.R requirements.txt
+RUN rm packages.R requirements.txt packages_test.R apsim-7592.deb
 
 ### Copying .bashrc of default $HOME directory to /opt
 RUN sudo cp .bashrc /opt/

jupyter-eiaspatial-notebook/jammy/packages.R

@@ -21,4 +21,4 @@ devtools::install_github(c("CIAT-DAPA/analogues",
                    "SantanderMetGroup/convertR",
                    "SantanderMetGroup/climate4R.indices",
                    "bakaburg1/BaySREn",
-                   "femiguez/apsimx"), configure.args="Ncpus = 4")
+                   "femiguez/apsimx"))

jupyter-eiaspatial-notebook/jammy/packages_test.R

@@ -0,0 +1,68 @@
+# This is just for testing if the R packages have been installed
+# How to run: source(packages_test.R)
+
+library('devtools')
+library('raster')
+library('shapefiles')
+library('ncdf4')
+library('terra')
+library('geodata')
+library('spatstat.geom')
+library('ggmap')
+library('rgee')
+library('leaflet')
+library('dismo')
+library('gdalUtilities')
+library('circlize')
+library('diagis')
+library('ggnewscale')
+library('lmerTest')
+library('lme4')
+library('metafor')
+library('metan')
+library('pbapply')
+library('FactoMineR')
+library('doParallel')
+library('ggpubr')
+library('broom')
+library('mlr3')
+library('RInside')
+library('doSNOW')
+library('Microsoft365R')
+library('googleCloudStorageR')
+library('circular')
+library('miceadds')
+library('multimode')
+library('sfsmisc')
+library('rJava')
+library('R.utils',)
+library('reshape2')
+library('rworldxtra')
+library('RCurl')
+library('tidyverse')
+library('ranger')
+library('sodium')
+library('pals')
+library('ggcorrplot')
+library('aws.s3')
+library('agricolae')
+library('xlsx')
+library('ecmwfr')
+library('Hmisc')
+library('envirem')
+library('maps')
+library('dplyr')
+library('DSSAT')
+library('rworldmap')
+
+library("analogues")
+library("loadeR.java")
+library("climate4R.UDG")
+library("loadeR")
+library("transformeR")
+library("visualizeR")
+library("downscaleR")
+library("convertR")
+library("climate4R.indices")
+library("BaySREn")
+library("apsimx")