Update README.md: Enhance usage instructions and add container setup details

README.md

@@ -1,6 +1,126 @@
-# R4_4_sing_container
+# R singularity/apptainer containers
 
 ## Usage
-Get this container using this command:
-`singularity pull oras://ghcr.io/kidcancerlab/r_4_4:latest`
 
+### You can run the container using these commands
+
+```bash
+# Make a workspace
+cd
+mkdir testrv
+
+# The rv cache needs to be outside of the container and bound to it, so we make a directory for it here.
+mkdir testrv/rv_cache
+cd testrv
+
+singularity pull oras://ghcr.io/kidcancerlab/r4_6_0:latest
+
+
+singularity shell \
+    --no-home \
+    --bind ~/testrv:/project \
+    --bind ~/testrv/rv_cache:/cache/rv \
+    r4_6_0_latest.sif
+```
+
+### inside of container
+
+This is needed on our cluster because $TMPDIR is set when I request a compute node.
+If $TMPDIR is set, rv will try to use it for caching and fail because it's not writable. Unsetting it allows rv to use the /cache/rv directory that we bind to the container, which is writable.
+```bash
+unset TMPDIR
+```
+
+### Then, you can initialize rv in the project directory and start adding packages to your rproject.toml file
+```bash
+cd /project
+
+rv init
+```
+
+update rproject.toml:
+```toml
+repositories = [
+  { alias = "CRAN", url = "https://cran.rstudio.com/" },
+  { alias = "PPM", url = "https://packagemanager.posit.co/cran/latest" },
+  { alias = "bioconductor", url = "https://bioconductor.org/packages/3.20/bioc" },
+  { alias = "BioCann", url = "https://bioconductor.org/packages/3.20/data/annotation"},
+  { alias = "BioCexp", url = "https://bioconductor.org/packages/3.20/data/experiment" },
+  { alias = "BioCworkflows", url = "https://bioconductor.org/packages/3.20/workflows"},
+]
+
+dependencies = [
+  "dplyr",
+]
+```
+
+### Use rv to install packages
+```bash
+rv plan
+
+rv sync
+```
+
+## Development
+To test a container out for development purposes, you can run the container in "sandbox" mode using this command:
+`singularity build --sandbox sing_sandbox oras://ghcr.io/kidcancerlab/r4_6_0:latest`
+
+Then, you can run the container using these commands:
+```bash
+cd
+mkdir testrv
+mkdir testrv/rv_cache
+cd testrv
+
+singularity shell \
+    --no-home \
+    --writable \
+    --fakeroot \
+    --bind ~/testrv:/project \
+    --bind ~/testrv/rv_cache:/cache/rv \
+    sing_sandbox
+
+mkdir sing_sandbox/project
+mkdir -p sing_sandbox/cache/rv
+```
+
+This lets you install or change things in the container and test them. Then, copy the relevant commands back to the .def file.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+## Misc
+I'm dropping this code here for later reference. It was generated by Gemini and I have not tested it, but I like the concept. It lets you run R code inside the container directly from a Quarto document.
+
+```{r setup, include=FALSE}
+# Define a custom knitr engine
+knitr::knit_engines$set(sing_r = function(options) {
+  # Collapse the chunk code into a single string
+  code <- paste(options$code, collapse = '\n')
+
+  # Wrap it in the apptainer command
+  # (Change the .sif name to match your actual container)
+  cmd <- sprintf("apptainer exec my_r_container.sif Rscript -e %s", shQuote(code))
+
+  # Execute the command and capture the output
+  out <- system(cmd, intern = TRUE)
+
+  # Return the properly formatted output back to Quarto
+  knitr::engine_output(options, options$code, out)
+})
+```
+```{sing_r}
+# do stuff inside the container
+print("Hello from inside the container!")
+```