add rocker sample

rocker/Dockerfile

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+FROM docker.io/rocker/rstudio:latest@sha256:ee7c4efa46f0b5d46e051393ef05f262aceb959463b15fc3648955965290d231
+
+USER root
+RUN mkdir /safe_data /safe_outputs /scratch /root/src
+
+COPY ./src /root/src
+
+WORKDIR /root/src
+
+RUN r install_packages.R

rocker/README.md

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+# TRE Rocker example
+
+## Running
+
+Run with `ces-run --debug --opt-file ./opt_file.txt` where `opt-file.txt` contains the following lines:
+
+```txt
+-p 8787:8787
+-e PASSWORD=test
+```
+
+Note that the password can be changed or left out entirely. In this case, the container will generate a new password to use, which will be printed in the same terminal where `ces-run` was called.
+
+## Notes
+
+This example takes a rocker image, creates the TRE file system directories and an extra directory for source files `src`. A script that produces a plot is copied inside `src`, along with another containing a list of required packages and a bash script to automate the test. The required packages are then installed through the script and the rstudio instance is started, which can be accessed at localhost:8787 using a browser.
+
+The user can run the code directly, create the plot and copy it to safe_outputs through the rstudio interface or run the `run_test.sh` script, which will perform these steps automatically.
+
+The container uses rootless mode operation by default (assumes that the user starting the container in the host is not root). When run using podman (as in `ces-run`) the login user is **root**, while in docker **rstudio**. Forcing a user change results in rstudio not starting.
+
+The example is tailored to podman, and the files are copied under the `/root/src` directory for ease of access when rstudio is first started. When using docker, they could for example be placed in `/home/rstudio/src` with appropriate permissions (the owner should be changed to the user **rstudio**).

rocker/src/install_packages.R

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+install.packages("ggplot2")

rocker/src/plot_example.R

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+# library
+library(ggplot2)
+
+# basic graph
+p <- ggplot(mtcars, aes(x = wt, y = mpg)) +
+  geom_point()
+
+# a data frame with all the annotation info
+annotation <- data.frame(
+   x = c(2,4.5),
+   y = c(20,25),
+   label = c("label 1", "label 2")
+)
+
+# Add text
+p + geom_text(data=annotation, aes( x=x, y=y, label=label),                 ,
+           color="orange",
+           size=7 , angle=45, fontface="bold" )
+
+ggsave("test_figure.png")

rocker/src/run_test.sh

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+#!/bin/bash
+
+cd /root/src
+
+# Run example script
+r plot_example.R
+
+# Copy output to /safe_outputs
+mv *.png /safe_outputs