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new ApsimX fix
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Odysseas Stefas committed Oct 23, 2024
1 parent 28bce74 commit 853cd69
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7 changes: 3 additions & 4 deletions jupyter-eiaspatial-notebook/jammy/Dockerfile
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Expand Up @@ -91,9 +91,8 @@ 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 2
RUN sudo apt-get update && sudo apt-get install libsqlite3-dev dotnet-sdk-6.0 -y
RUN sudo apt-get install gtk-sharp3 libgtksourceview-4-0 zenity -y
# 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

Expand Down Expand Up @@ -122,7 +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

### Copying .bashrc of default $HOME directory to /opt
RUN sudo cp .bashrc /opt/
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2 changes: 1 addition & 1 deletion jupyter-eiaspatial-notebook/jammy/packages.R
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Expand Up @@ -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"), configure.args="Ncpus = 1")
68 changes: 68 additions & 0 deletions jupyter-eiaspatial-notebook/jammy/packages_test.R
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@@ -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")

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