Update 2025 06

README.md

@@ -91,27 +91,66 @@ The instances are created using the EC2 client of AWS CLI. Into the `./infrastru
 ```jsx
 {
   ImageId: 'ami-0130bec6e5047f596', // this iam can be found right to the name of the instance when a new instance is launched by hand, this id is unique by region
-  InstanceType: 't2.micro', // size of the instance
+  InstanceType: 't3.micro', // size of the instance
   KeyName: KEY_NAME,
   MaxCount: 1,
   MinCount: 1,
   SecurityGroupIds: [SECURTY_GROUP], // security group created on step 3
   IamInstanceProfile: {
     Name: INSTANCE_PROFILE,
   },
+  BlockDeviceMappings: [
+    {
+      DeviceName: '/dev/sda1',
+      Ebs: {
+        DeleteOnTermination: true,
+        VolumeSize: 16, // size in GB
+        VolumeType: 'gp3',
+      },
+    },
+  ],
   UserData: `#!/bin/bash
     sudo mkdir /home/ubuntu/docker-runner
     cd /home/ubuntu/docker-runner
     sudo chown -R $USER:$USER /home/ubuntu/docker-runner
+
+    # Add Docker's official GPG key:
+    sudo apt-get update
+    sudo apt-get install -y ca-certificates curl
+    sudo install -m 0755 -d /etc/apt/keyrings
+    sudo curl -fsSL https://download.docker.com/linux/ubuntu/gpg -o /etc/apt/keyrings/docker.asc
+    sudo chmod a+r /etc/apt/keyrings/docker.asc
+
+    # Add the repository to Apt sources:
+    echo \
+      "deb [arch=$(dpkg --print-architecture) signed-by=/etc/apt/keyrings/docker.asc] https://download.docker.com/linux/ubuntu \
+      $(. /etc/os-release && echo "$VERSION_CODENAME") stable" | \
+      sudo tee /etc/apt/sources.list.d/docker.list > /dev/null
     sudo apt-get update
-    sudo apt install docker -y
-    sudo apt install docker.io -y
-    sudo service docker start
-    sudo chmod 666 /var/run/docker.sock
-    sudo apt install awscli -y
+
+    # install Docker
+    sudo apt-get install -y docker-ce docker-ce-cli containerd.io docker-buildx-plugin docker-compose-plugin
+
+    # add current user to "docker" group (to allow running docker without sudo)
+    sudo usermod -aG docker $USER
+    newgrp docker
+
+    # install AWS CLI
+    sudo apt-get install -y unzip
+    curl "https://awscli.amazonaws.com/awscli-exe-linux-x86_64.zip" -o "awscliv2.zip"
+    unzip awscliv2.zip
+    sudo ./aws/install
+    rm -r aws
+    rm awscliv2.zip
+
+    # login to Amazon ECR
     aws ecr get-login-password --region ${REGION} | docker login --username AWS --password-stdin ${ACCOUNT}
-    docker pull ${ACCOUNT}/rstudio
-    sudo docker run -d -p 8787:8787 -e DISABLE_AUTH=true ${ACCOUNT}/rstudio
+
+    # pull rstudio image
+    docker pull ${ACCOUNT}/rstudio:1.1
+
+    # run rstudio container
+    sudo docker run -d -p 8787:8787 -e DISABLE_AUTH=true --restart always ${ACCOUNT}/rstudio:1.1
  `,
   TagSpecifications: [
     {
@@ -235,7 +274,7 @@ Procfile
     STRING_TO_REPLACE: process.env.STRING_TO_REPLACE,
     ROUTE_TO_REPLACE: process.env.ROUTE_TO_REPLACE,
     TIMEOUT_INSTANCE: process.env.TIMEOUT_INSTANCE,
-    PROXY_KEY: process.env.PROXY_KEY
+    PROXY_KEY: process.env.PROXY_KEY,
   }
   ```
 
@@ -274,7 +313,7 @@ module.exports = {
   ROUTE_TO_REPLACE: process.env.ROUTE_TO_REPLACE,
   STRING_TO_REPLACE: process.env.STRING_TO_REPLACE,
   TIMEOUT_INSTANCE: process.env.TIMEOUT_INSTANCE,
-  PROXY_KEY: process.env.PROXY_KEY
+  PROXY_KEY: process.env.PROXY_KEY,
 }
 ```
 

RStudioDocker/Dockerfile

@@ -1,48 +1,86 @@
-FROM rocker/rstudio:latest
+FROM rocker/rstudio:4.5.1
 
 RUN apt-get update
 # RUN apt-get remove libpq5 -y
-RUN apt-get install libpq-dev r-cran-rgl -y
+RUN apt-get install -y \
+    default-jre \
+    default-jdk \
+    libpq-dev \
+    libxml2-dev \
+    libudunits2-dev \
+    libgeos-dev \
+    libglu1-mesa-dev \
+    r-cran-rgl \
+    r-cran-rjava
+
+RUN R CMD javareconf
+
+RUN apt-get install -y \
+    libcairo2-dev \
+    libgdal-dev \
+    libfontconfig1-dev \
+    libgit2-dev \
+    libglu1-mesa-dev \
+    libproj-dev \
+    r-cran-hmisc \
+    r-cran-rodbc \
+    r-cran-vegan \
+    unixodbc \
+    unixodbc-dev
+# libiodbc2-dev \
 
-RUN install2.r --error dplyr
 RUN install2.r --error \
-    sqldf \
-    jsonlite \
     httr \
+    jsonlite \
+    sqldf \
     zip
-    
+
 RUN install2.r --error -r 'http://cran.r-project.org'  \
     data.table \
     desc \
     dplyr \
-    RPostgreSQL \
-    reshape \
-    reshape2 \
-    random \
-    gsubfn \
+    DT \
     evaluate \
     Formula \
+    ggExtra \
+    gsubfn \
+    Hmisc \
+    jpeg \
     knitr \
+    lattice \
     lazyeval \
     locfit \
-    DataCombine \
+    lmfor \
+    markdown \
+    nortest \
+    outliers \
+    png \
+    random \
+    rentrez \
+    reshape \
+    reshape2 \
+    rlang \
+    rmarkdown \
+    RPostgreSQL \
     RSQLite \
-    rmarkdown
-
-RUN apt-get install -y r-cran-rjava default-jre default-jdk libxml2-dev libudunits2-dev libgeos-dev
-RUN R CMD javareconf
-
-RUN install2.r --error -r 'http://cran.r-project.org' XLConnect rentrez
-RUN install2.r --error -r 'http://cran.r-project.org' lmfor survey survival DT lattice png jpeg vegan sampling sp markdown nortest outliers SamplingBigData scales spatial whisker
-
-RUN apt-get install -y libglu1-mesa-dev 
-RUN apt-get install -y libiodbc2-dev
-RUN apt-get install -y unixodbc unixodbc-dev r-cran-rodbc libgdal-dev libproj-dev
-RUN apt-get install -y r-cran-hmisc libfontconfig1-dev libcairo2-dev
-RUN apt-get install -y libgit2-dev r-cran-vegan
+    sampling \
+    SamplingBigData \
+    scales \
+    sp \
+    spatial \
+    stringr \
+    srvyr \
+    survey \
+    survival \
+    vegan \
+    whisker \
+    XLConnect
+#    BIOMASS \
+#    DataCombine \
+#    rgdal \
+#    sf \
 
-RUN install2.r --error -r 'http://cran.r-project.org' sf rgdal
-RUN install2.r --error -r 'http://cran.r-project.org' Hmisc
-RUN install2.r --error -r 'https://mac.R-project.org' mapview
-RUN install2.r --error -r 'http://cran.r-project.org' ggExtra BIOMASS
+# RUN install2.r --error -r 'https://mac.R-project.org' mapview
 
+RUN apt-get autoclean -y
+RUN apt-get autoremove -y