use pam-helper as auth, change to port 8080

Author: andreyhgl

Dockerfile

@@ -25,5 +25,5 @@ RUN R -e "remotes::install_github('chris-mcginnis-ucsf/DoubletFinder@3b420df68b8
 COPY ./start-rserver.sh /usr/local/bin/start-rserver.sh
 RUN chmod +x /usr/local/bin/start-rserver.sh
 
-EXPOSE 8787
+EXPOSE 8080
 CMD ["/usr/local/bin/start-rserver.sh"]

README.md

@@ -8,25 +8,43 @@
 5. Open a browser and run Rstudio
 
 
-```
+```sh
 # On the HPC (from an interactive job or within a SLURM submission)
-#PORT=$(shuf -i 10000-20000 -n 1)
-PORT=13337
-echo "RStudio on $(hostname):$PORT"
-
 apptainer run \
   --cleanenv \
-  --env RSTUDIO_PORT=$PORT \
+  --env RSTUDIO_PORT=8080 \
   --env RSTUDIO_ADDRESS=0.0.0.0 \
-  docker://ghcr.io/karlssonlaboratory/rstudio-server:latest
+  docker://ghcr.io/karlssonlaboratory/rstudio-server:c46e9ec > ~/rserver.log 2>&1
 ```
 
 ```
-#ssh -N -L 8787:<compute-node>:$PORT <remote-host>
-# open http://localhost:8787
+ssh -v -N -L 8080:p108:8080 pelle
+# open http://localhost:9876
 ```
 
 
 ```
- ghcr.io/karlssonlaboratory/rstudio-server:latest
+ ghcr.io/karlssonlaboratory/rstudio-server:c46e9ec
+```
+
+```sh
+# On the HPC (from an interactive job or within a SLURM submission)
+mkdir -p test_dir/marimo_test
+cd test_dir/marimo_test
+
+ml pixi-tools
+
+pixi init -c conda-forge -c bioconda
+pixi add python
+pixi add --pypi marimo
+pixi shell
+marimo edit --headless --host 0.0.0.0 --port 8080
+```
+
+```sh
+ssh -L 8080:p108:8080 pelle
+```
+
+```sh
+http://0.0.0.0:8080
 ```

start-rserver.sh

@@ -1,49 +1,40 @@
 #!/usr/bin/env bash
 set -euo pipefail
 
-PORT="${RSTUDIO_PORT:-8787}"
+PORT="${RSTUDIO_PORT:-8080}"
 ADDRESS="${RSTUDIO_ADDRESS:-0.0.0.0}"
+USER_NAME="$(id -un)"
+WORKDIR="${RSTUDIO_TMPDIR:-$HOME/.rstudio-server-run}"
 
-if [ "$(id -u)" -eq 0 ]; then
-  # --- Docker path: running as root, use rocker's built-in init ---
-  # rocker/rstudio ships /init which sets up the rstudio user and launches rserver.
-  # Honor a password if provided, otherwise disable auth (only safe behind a tunnel).
-  export PASSWORD="${PASSWORD:-}"
-  if [ -z "$PASSWORD" ]; then
-    export DISABLE_AUTH=true
-  fi
-  exec /init
+mkdir -p "$WORKDIR"/{run,lib,log,tmp}
 
-else
-  # --- Apptainer path: rootless, everything must live under $HOME ---
-  USER_NAME="$(id -un)"
-  USER_ID="$(id -u)"
-  WORKDIR="${RSTUDIO_TMPDIR:-$HOME/.rstudio-server-run}"
-  mkdir -p "$WORKDIR"/{run,lib,log,tmp}
-
-  COOKIE_KEY="$WORKDIR/secure-cookie-key"
-  if [ ! -s "$COOKIE_KEY" ]; then
-    uuidgen > "$COOKIE_KEY"
-    chmod 0600 "$COOKIE_KEY"
-  fi
+# Generate a password if not supplied
+if [ -z "${PASSWORD:-}" ]; then
+  PASSWORD=$(openssl rand -base64 15)
+  echo "=================================================="
+  echo "RStudio login:"
+  echo "  User:     $USER_NAME"
+  echo "  Password: $PASSWORD"
+  echo "=================================================="
+fi
+export PASSWORD
 
-  cat > "$WORKDIR/database.conf" <<EOF
+# rserver wants this in a .conf file too
+cat > "$WORKDIR/database.conf" <<EOF
 provider=sqlite
 directory=$WORKDIR/lib
 EOF
 
-  cat > "$WORKDIR/rserver.conf" <<EOF
-www-port=$PORT
-www-address=$ADDRESS
-www-verify-user-agent=0
-auth-none=1
-auth-minimum-user-id=$USER_ID
-server-user=$USER_NAME
-server-data-dir=$WORKDIR/run
-secure-cookie-key-file=$COOKIE_KEY
-database-config-file=$WORKDIR/database.conf
-server-daemonize=0
-EOF
-
-  exec /usr/lib/rstudio-server/bin/rserver --config-file="$WORKDIR/rserver.conf"
-fi
+exec /usr/lib/rstudio-server/bin/rserver \
+  --www-port="$PORT" \
+  --www-address="$ADDRESS" \
+  --www-verify-user-agent=0 \
+  --auth-none=0 \
+  --auth-pam-helper-path=pam-helper \
+  --auth-stay-signed-in-days=30 \
+  --auth-timeout-minutes=0 \
+  --server-user="$USER_NAME" \
+  --server-data-dir="$WORKDIR/run" \
+  --database-config-file="$WORKDIR/database.conf" \
+  --secure-cookie-key-file="$WORKDIR/secure-cookie-key" \
+  --server-daemonize=0