diff --git a/bih-cluster/docs/ondemand/interactive.md b/bih-cluster/docs/ondemand/interactive.md
index 1ba1f7dc9..21ba84ba3 100644
--- a/bih-cluster/docs/ondemand/interactive.md
+++ b/bih-cluster/docs/ondemand/interactive.md
@@ -108,63 +108,63 @@ To use the OnDemand portal with a specific R installation including a stable set
For this you may first need to create this conda environment including your R version of choice and all necessary packages. Specific installations of i.e. python from conda can be used similarly in other interactive apps.
- For reproducibility this environment should clearly define all package versions and include dependencies. This is easiest to achieve by first collecting all packages you need into a primary collection (i.e. a yaml file, potentially including a specific R version for r-base if needed) and creating an environment from there. Exporting this environment will generate a file with all used packages and their version numbers, that can be used to recreate the same environment.
-- Example code
-
-
- Click to expand
-
- * Commands:
- + `conda env create -n R-example -f R-example.yaml`
- + `conda activate R-example`
- + `conda env export -f R-fixed-versions.yaml`
- + `conda env create -n R-fixed-versions -f R-fixed-versions.yaml`
- * R-example.yaml
-
- ```
- channels:
- - conda-forge
- - bioconda
- - defaults
- dependencies:
- - r-base
- - r-essentials
- - r-devtools
- - bioconductor-deseq2
- - r-tidyverse
- - r-rmarkdown
- - r-knitr
- - r-dt
- ```
-
+- Example code:
+
+
+Click to expand
+
+* Commands:
+ + `conda env create -n R-example -f R-example.yaml`
+ + `conda activate R-example`
+ + `conda env export -f R-fixed-versions.yaml`
+ + `conda env create -n R-fixed-versions -f R-fixed-versions.yaml`
+* R-example.yaml
+
+```
+channels:
+ - conda-forge
+ - bioconda
+ - defaults
+dependencies:
+ - r-base
+ - r-essentials
+ - r-devtools
+ - bioconductor-deseq2
+ - r-tidyverse
+ - r-rmarkdown
+ - r-knitr
+ - r-dt
+```
+
- R packages only available from github
Some packages (i.e. several single-cell-RNAseq analysis tools) are only available from github and not on Cran/Bioconductor. There are two ways to install such packages into a conda enviroment.
-
- Click to expand
+
+Click to expand
- 1) Install from inside R \[easier option, but not pure conda\]
+1) Install from inside R \[easier option, but not pure conda\]
- * First setup the conda env, ideally including all dependencies for the desired package from github (and do include r-devtools)
- * Then within R run `devtools::install_github('owner/repo', dependencies=F, upgrade=F, lib='/path/to/conda/env-name/lib/R/library')`
- * if you don't have all dependencies already installed you will have to omit dependencies=F and risk a mix of conda & native R installed packages (or just have to redo the conda env).
- * github_install involves a build process and still needs a bit of memory, so this might crash on the default `srun --pty bash -i` shell
+* First setup the conda env, ideally including all dependencies for the desired package from github (and do include r-devtools)
+* Then within R run `devtools::install_github('owner/repo', dependencies=F, upgrade=F, lib='/path/to/conda/env-name/lib/R/library')`
+* if you don't have all dependencies already installed you will have to omit dependencies=F and risk a mix of conda & native R installed packages (or just have to redo the conda env).
+* github_install involves a build process and still needs a bit of memory, so this might crash on the default `srun --pty bash -i` shell
- 2) Build packages into a local conda channel \[takes longer, but pure conda\]\
- This approach is mostly taken from the answers given [here](https://stackoverflow.com/questions/52061664/install-r-package-from-github-using-conda). These steps must be taken _before_ building the final env used with Rstudio
+2) Build packages into a local conda channel \[takes longer, but pure conda\]\
+ This approach is mostly taken from the answers given [here](https://stackoverflow.com/questions/52061664/install-r-package-from-github-using-conda). These steps must be taken _before_ building the final env used with Rstudio
- * use `conda skeleton cran https://github.com/owner/repo [--git-tag vX.Y]` to generate build files
- * conda skeleton only works for repositories with a release/version tag. If the package you want to install does not have that, you either need to create a fork and add a such a tag, or find a fork that already did that. Downloading the code directly from github and building the package from that is also possible, but you will the need to manually set up the `meta.yaml` and `build.sh` files that conda skeleton would create.
- * If there is more than one release tag, do specify which one you want, it may not automatically take the most recent one.
- * If any r-packages from bioconductor are dependencies, conda will not find them during the build process. You will need to change the respective entries in the `meta.yaml` file created by conda skeleton. I.e. change `r-deseq2` to `bioconductor-deseq2`
- * Build the package with `conda build --R= [--use-local] r-`
- * You need to specifying the same R-version used in the final conda env
- * If the github package has additional dependencies from github, build those first and then add `--use-local` so the build process can find them.
- * The build process definitely needs more memory than the default `srun --pty bash -i` shell. It also takes quite a bit of time (much longer than installing through devtools::install_github)
- * Finally add the packages (+versions) you built to the environment definition (i.e. yaml file) and create the (final) conda environment. Don't forget to tell conda to use locally build packages (either supply `--use-local` or add `- local` to the channel list in the yaml file)
+* use `conda skeleton cran https://github.com/owner/repo [--git-tag vX.Y]` to generate build files
+ * conda skeleton only works for repositories with a release/version tag. If the package you want to install does not have that, you either need to create a fork and add a such a tag, or find a fork that already did that. Downloading the code directly from github and building the package from that is also possible, but you will the need to manually set up the `meta.yaml` and `build.sh` files that conda skeleton would create.
+ * If there is more than one release tag, do specify which one you want, it may not automatically take the most recent one.
+ * If any r-packages from bioconductor are dependencies, conda will not find them during the build process. You will need to change the respective entries in the `meta.yaml` file created by conda skeleton. I.e. change `r-deseq2` to `bioconductor-deseq2`
+* Build the package with `conda build --R= [--use-local] r-`
+ * You need to specifying the same R-version used in the final conda env
+ * If the github package has additional dependencies from github, build those first and then add `--use-local` so the build process can find them.
+ * The build process definitely needs more memory than the default `srun --pty bash -i` shell. It also takes quite a bit of time (much longer than installing through devtools::install_github)
+* Finally add the packages (+versions) you built to the environment definition (i.e. yaml file) and create the (final) conda environment. Don't forget to tell conda to use locally build packages (either supply `--use-local` or add `- local` to the channel list in the yaml file)
-
+
Starting the Rstudio session via the OnDemand portal works almost as described above (see Example 1). However, you do have to select \`miniconda\` as R source and provide the path to your miniconda installation and (separated by a colon) the name of the (newly created) conda enviroment you want to use.