Merge pull request #12 from grst/podman

Podman version

README.md

@@ -1,65 +1,137 @@
-# Howto run Rstudio Server in a Conda Environment
+# Running Rstudio Server in a Conda Environment
 
-I usually rely on the [conda package manager]() to manage my environments during development. Thanks to [conda-forge](https://conda-forge.org/) and [bioconda](https://bioconda.github.io/) most R packages are now also available through conda. 
+I usually rely on the [conda package manager](https://docs.conda.io/en/latest/) to manage my environments during development. Thanks to [conda-forge](https://conda-forge.org/) and [bioconda](https://bioconda.github.io/) most R packages are now also available through conda. For production,
+I [convert them to containers](https://github.com/grst/containerize-conda) as these are easier to share. 
 
-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 is why I came up with the two scripts in this repo. 
+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. 
 
-## Installation and usage
-### 1. Prerequisites
-* installed [rstudio server](https://www.rstudio.com/products/rstudio/download-server/)
-* installed [conda](https://docs.conda.io/en/latest/miniconda.html)
+## Running Rstudio Server in a Container
 
-### 2. Disable rstudio server service. 
-You might need to disable the system-wide Rstudio server service.
-Due to licensing restrictions of rstudio server community edition, only one rstudio process
-can run for each user simultaneously. 
+With this approach Rstudio Server runs in a Docker container (based on [rocker/rstudio](https://hub.docker.com/r/rocker/rstudio)).  
+The conda environment gets mounted into the container - like that there's no need to rebuild the container to add a package and 
+`install.packages` can be used without issues. The container-based approach has the following benefits: 
 
-This is how it works on systemd-based systems:
+ * Authentication works (#3)
+ * Several separate instances of Rstudio server can run in parallel, even without the *Pro* version. 
 
-```bash
-sudo systemctl disable rstudio-server.service
-sudo systemctl stop rstudio-server.service
-```
+### Prerequisites
 
-### 3. Clone this repo
-```
-git clone https://github.com/grst/rstudio-server-conda.git
-```
+ * [Docker](https://www.docker.com/) or [Podman](https://podman.io/)
+ * [docker-compose](https://github.com/docker/compose) or [podman-compose](https://github.com/containers/podman-compose)
+ * [conda](https://docs.conda.io/en/latest/miniconda.html) or [mamba](https://github.com/conda-forge/miniforge#mambaforge)
 
-### 4. Run rstudio server in the conda env
-```
-conda activate my_project
-./start_rstudio_server.sh 8787  # use any free port number here. 
-```
+### Usage
 
-You should now be able to connect to rstudio server on the port you specify. **If an R Session has previously been running, you'll need to rstart the Rsession now**. 
+1. Clone this repository
 
-Obviously, if your env does not have a version of `R` installed, this will either not 
-work at all, or fall back to the system-wide R installation. 
+   ```bash
+   git clone [email protected]:grst/rstudio-server-conda.git
+   ```
 
+2. Build the rstudio container (fetches the latest version of [rocker/rstudio](https://hub.docker.com/r/rocker/rstudio) and adds some custom scripts)
 
+   ```bash
+   cd rstudio-server-conda/docker
+   docker-compose build     # or podman-compose
+   ```
 
-## How it works
+3. Copy the docker-compose.yml file into your project directory and adjust the paths.
+
+   You may want to add additional volumes with your data. 
+
+   ```yml
+   [...]
+      ports:
+         # port on the host : port in the container (the latter is always 8787)
+         - "8889:8787"
+       volumes:
+         # mount conda env into exactely the same path as on the host system - some paths are hardcoded in the env.
+         - /home/sturm/anaconda3/envs/R400:/home/sturm/anaconda3/envs/R400
+         # Share settings between rstudio instances
+         - /home/sturm/.local/share/rstudio/monitored/user-settings:/root/.local/share/rstudio/monitored/user-settings
+         # mount the working directory containing your R project.
+         - /home/sturm/projects:/projects
+       environment:
+         # password used for authentication
+         - PASSWORD=notsafe
+         # repeat the path of the conda environment (must be identical to the path in "volumes")
+         - CONDAENV=/home/sturm/anaconda3/envs/R400
+   ```
+
+4. Run your project-specific instance of Rstudio-server
+
+   ```bash
+   docker-compose up 
+   ```
+
+5. Log into Rstudio
+
+ * Open your server at `https://localhost:8889` (or whatever port you specified)
+ * Login with the user `rstudio` (when using Docker) or `root` (when using Podman) and the password you specified 
+   in the `docker-compose.yml`. If you are using Podman and login with `rstudio` you won't have permissions to 
+   access the mounted volumes. 
+
+
+## Running Locally
+
+With this approach a locally installed Rstudio server is ran such that it uses the conda env. 
+A known limitation of this approch is that the Rstudio authentication is bypassed (see #3). 
+Therefore, only use this approach in a secure network! 
+
+### Prerequisites
+* [rstudio server](https://www.rstudio.com/products/rstudio/download-server/) installed locally
+* [conda](https://docs.conda.io/en/latest/miniconda.html) or [mamba](https://github.com/conda-forge/miniforge#mambaforge)
+
+### Usage
+
+1. Clone this repo
+
+   ```
+   git clone https://github.com/grst/rstudio-server-conda.git
+   ```
+
+2. Run rstudio server in the conda env
+
+   ```
+   cd rstudio-server-conda/local
+   conda activate my_project
+   ./start_rstudio_server.sh 8787  # use any free port number here. 
+   ```
+   
+3. Connect to Rstudio
+
+   You should now be able to connect to rstudio server on the port you specify. 
+   **If an R Session has previously been running, you'll need to rstart the Rsession now**. 
+
+   Obviously, if your env does not have a version of `R` installed, this will either not 
+   work at all, or fall back to the system-wide R installation. 
+
+
+### How it works
 * Rstudio server, can be started in non-daemonized mode by each user individually on a custom port (similar to a jupyter notebook). This instance can then run in a conda environment:
-```
-> conda activate my_project
-> /usr/lib/rstudio-server/bin/rserver \
-   --server-daemonize=0 \
-   --www-port 8787 \
-   --rsession-which-r=$(which R) \
-   --rsession-ld-library-path=$CONDA_PREFIX/lib
-```
+
+   ```
+   > conda activate my_project
+   > /usr/lib/rstudio-server/bin/rserver \
+      --server-daemonize=0 \
+      --www-port 8787 \
+      --rsession-which-r=$(which R) \
+      --rsession-ld-library-path=$CONDA_PREFIX/lib
+   ```
+
 * To avoid additional problems with library paths, also `rsession` needs to run within the conda environment. This is achieved by wrapping `rsession` into the [rsession.sh](https://github.com/grst/rstudio-server-conda/blob/master/rsession.sh) script. The path to the wrapped `rsession` executable can be passed to `rserver` as command line argument. 
-```
-rserver # ...
-    --rsession-path=rsession.sh
-```
+
+   ```
+   rserver # ...
+       --rsession-path=rsession.sh
+   ```
 
 
 * When using multiple users a unique `secret-cookie-key` has to be generated for each user. The path to the secret cookie key can be passed to `rserver` as a command line parameter.
-```
-uuid > /tmp/rstudio-server/${USER}_secure-cookie-key
-rserver # ...
-  --secure-cookie-key-file /tmp/rstudio-server/${USER}_secure-cookie-key
-```
+
+   ```
+   uuid > /tmp/rstudio-server/${USER}_secure-cookie-key
+   rserver # ...
+     --secure-cookie-key-file /tmp/rstudio-server/${USER}_secure-cookie-key
+   ```
 

docker/Dockerfile

@@ -0,0 +1,8 @@
+FROM rocker/rstudio
+
+ENV ROOT=TRUE
+ENV LANG=C.UTF-8 LC_ALL=C.UTF-8
+
+ADD init2.sh /init2.sh
+
+CMD ["/init2.sh"]

docker/README.md

@@ -0,0 +1,13 @@
+# Rstudio server conda (podman version)
+
+## Usage:
+
+ * copy the docker-compose.yml file into your project directory
+ * update the conda env paths and port in docker-compose.yml
+ * `podman-compose up`
+
+## Note:
+ * when using docker, login with the `rstudio` user as described on the "rocker"
+   page. 
+ * when using podman, login with the `root` user, as root within the container
+   corresponds to your user outside the container. 

docker/docker-compose.yml

@@ -0,0 +1,21 @@
+version: "3.9"
+services:
+  rstudio:
+    build: .
+    image: grst/rstudio-server-conda:latest
+    ulimits:
+      nofile: 10000
+    ports:
+      - "8889:8787"
+    volumes:
+      # mount conda env into exactely the same path as on the host system - some paths are hardcoded in the env.
+      - /home/sturm/anaconda3/envs/R400:/home/sturm/anaconda3/envs/R400
+      # Share settings between rstudio instances
+      - /home/sturm/.local/share/rstudio/monitored/user-settings:/root/.local/share/rstudio/monitored/user-settings
+      # mount the working directory containing your R project.
+      - /home/sturm/projects:/root/projects
+    environment:
+      - PASSWORD=notsafe
+      # repeat the path of the conda environment
+      - CONDAENV=/home/sturm/anaconda3/envs/R400
+

docker/init2.sh

@@ -0,0 +1,19 @@
+#!/bin/bash
+
+# Settings required for conda+rstudio
+export RSTUDIO_WHICH_R=${CONDAENV}/bin/R
+export RETICULATE_PYTHON=${CONDAENV}/bin/python
+echo rsession-which-r=${RSTUDIO_WHICH_R} > /etc/rstudio/rserver.conf
+echo rsession-ld-library-path=${CONDAENV}/lib >> /etc/rstudio/rserver.conf
+echo "R_LIBS_USER=${CONDAENV}/lib/R/library" > /home/rstudio/.Renviron
+# Set root password (with podman, we need to login as root rather than "rstudio")
+echo "root:$PASSWORD" | chpasswd
+echo "auth-minimum-user-id=0" >> /etc/rstudio/rserver.conf
+
+# Custom settings
+echo "session-timeout-minutes=0" > /etc/rstudio/rsession.conf
+echo "auth-timeout-minutes=0" >> /etc/rstudio/rserver.conf
+echo "auth-stay-signed-in-days=30" >> /etc/rstudio/rserver.conf
+
+# Run original rocker launcher script
+/init