Singularity version

README.md

@@ -5,9 +5,23 @@ I [convert them to containers](https://github.com/grst/containerize-conda) as th
 
 Unfortunately, there seems to be [no straightforward way](https://community.rstudio.com/t/start-rstudio-server-session-in-conda-environment/12516/15) to use conda envs in Rstudio server. This repository provides two approaches to make rstudio server work with conda envs. 
 
- * [Running Rstudio Server in a Container](#running-rstudio-server-in-a-container)
+ * [Running Rstudio Server in a Singularity Container](#running-rstudio-server-in-singularity)
+ * [Running Rstudio Server in a Docker/Podman Container](#running-rstudio-server-in-a-container)
  * [Running Rstudio Server locally](#running-locally)
 
+## Running Rstudio Server in Singularity
+
+### Prerequisites
+
+ * [Singularity]
+ * [conda]
+
+### Usage
+
+ 1. Activate the target conda env or set the environment variable `CONDA_PREFIX`
+    to point to the location of the conda env. 
+ 2. 
+
 ## Running Rstudio Server in a Container
 
 With this approach Rstudio Server runs in a Docker container (based on [rocker/rstudio](https://hub.docker.com/r/rocker/rstudio)).  

singularity/.gitignore

@@ -0,0 +1,5 @@
+*.sif
+var-lib-rstudio-server
+run
+tmp
+

singularity/Singularity

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+Bootstrap: docker
+
+From: rocker/rstudio
+
+%files
+    init.sh /init.sh
+
+%post
+    echo "lock-type=linkbased" > /etc/rstudio/file-locks
+    chmod +x /init.sh
+    wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda.sh
+    bash ~/miniconda.sh -b -p /opt/conda
+
+
+

singularity/database.conf

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+provider=sqlite
+directory=/var/lib/rstudio-server

singularity/init.sh

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+#!/bin/bash
+
+source /opt/conda/etc/profile.d/conda.sh && \
+  conda activate $CONDA_PREFIX && \
+  rserver \
+    --www-address=127.0.0.1 \
+    --www-port=$PORT \
+    --rsession-which-r=$RSTUDIO_WHICH_R \
+    --rsession-ld-library-path=$CONDA_PREFIX/lib \
+    `# optional: old behaviour of R sessions` \
+    --auth-timeout-minutes=0 --auth-stay-signed-in-days=30  \
+    `# activate password authentication` \
+    --auth-none=0  --auth-pam-helper-path=pam-helper
+

singularity/rsession.conf

@@ -0,0 +1 @@
+# add your configuration here

singularity/run_singularity.sh

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+#!/bin/bash
+
+# See also https://www.rocker-project.org/use/singularity/
+
+# Main parameters for the script with default values
+PORT=${PORT:-8787}
+PASSWORD=${PASSWORD:-notsafe}
+TMPDIR=${TMPDIR:-tmp}
+CONTAINER="rstudio_latest.sif"  # path to singularity container (will be automatically downloaded)
+
+# Set-up temporary paths
+RSTUDIO_TMP="${TMPDIR}/$(echo -n $CONDA_PREFIX | md5sum | awk '{print $1}')"
+mkdir -p $RSTUDIO_TMP/{run,var-lib-rstudio-server,local-share-rstudio}
+
+R_BIN=$CONDA_PREFIX/bin/R
+PY_BIN=$CONDA_PREFIX/bin/python
+
+if [ ! -f $CONTAINER ]; then
+	singularity build --fakeroot $CONTAINER Singularity
+fi
+
+if [ -z "$CONDA_PREFIX" ]; then
+  echo "Activate a conda env or specify \$CONDA_PREFIX"
+  exit 1
+fi
+
+echo "Starting rstudio service on port $PORT ..."
+singularity exec \
+	--bind $RSTUDIO_TMP/run:/run \
+	--bind $RSTUDIO_TMP/var-lib-rstudio-server:/var/lib/rstudio-server \
+  --bind /sys/fs/cgroup/:/sys/fs/cgroup/:ro \
+	--bind database.conf:/etc/rstudio/database.conf \
+	--bind rsession.conf:/etc/rstudio/rsession.conf \
+  --bind $RSTUDIO_TMP/local-share-rstudio:/home/rstudio/.local/share/rstudio \
+	--bind ${CONDA_PREFIX}:${CONDA_PREFIX} \
+	--bind $HOME/.config/rstudio:/home/rstudio/.config/rstudio \
+  `# add additional bind mount required for your use-case` \
+  --bind /data:/data \
+  --env CONDA_PREFIX=$CONDA_PREFIX \
+	--env RSTUDIO_WHICH_R=$R_BIN \
+	--env RETICULATE_PYTHON=$PY_BIN \
+	--env PASSWORD=$PASSWORD \
+  --env PORT=$PORT \
+	rstudio_latest.sif \
+  /init.sh
+
+