fix

Author: uniqueg

README.md

@@ -51,25 +51,18 @@ zarp \
 Quick installation requires the following:
 
 - Linux with root permissions
-- [`conda >= 22.11.1`][conda]
-- [`mamba >=1.3.0`][mamba]
+- [`conda >= 24.11.3`][conda]
+- Recommended: [`apptainer >= 1.3.6`][apptainer] (only required if `APPTAINER`
+  shall be used as the dependency embedding strategy)
 
 Execute the following commands:
 
 ```sh
 git clone git@github.com:zavolanlab/zarp
 git clone git@github.com:zavolanlab/zarp-cli.git
 cd zarp-cli
-mamba env create -f install/environment.root.yml
+conda env create -f install/environment.yml
 conda activate zarp-cli
-```
-
-> If you do not have root privileges on your machine, replace the `mamba env
-> create` call with the following one:
->
-> ```sh
-> mamba env create -f install/environment.yml
-> ```
 
 That's it - you can now use _ZARP-cli_!
 
@@ -103,6 +96,7 @@ by [email][contact].
 
 © 2021 [Zavolab, Biozentrum, University of Basel][zavolab]
 
+[apptainer]: <https://apptainer.org/>
 [conda]: <https://docs.conda.io/projects/conda/en/latest/index.html>
 [contact]: <mailto:zavolab-biozentrum@unibas.ch>
 [badge-build-status]: <https://github.com/zavolanlab/zarp-cli/actions/workflows/tests.yml/badge.svg>
@@ -121,7 +115,6 @@ by [email][contact].
 [badge-url-license]: <http://www.apache.org/licenses/LICENSE-2.0>
 [htsinfer]: <https://github.com/zavolanlab/htsinfer>
 [issue-tracker]: <https://github.com/zavolanlab/zarp-cli/issues>
-[mamba]: <https://mamba.readthedocs.io/en/latest/>
 [semver]: <https://semver.org/>
 [zarp]: <https://github.com/zavolanlab/zarp>
 [zavolab]: <https://www.biozentrum.unibas.ch/research/researchgroups/overview/unit/zavolan/research-group-mihaela-zavolan/>

docs/guides/installation.md

@@ -6,30 +6,57 @@ On this page, you will find out how to install _ZARP-cli_ on your system.
 
 Installation requires the following:
 
-- Linux (tested with Ubuntu 20.04; macOS has not been tested yet)
-- [Conda][conda] (tested with `conda 22.11.1`)
-- [Mamba][mamba] (tested with `mamba 1.3.0`)
-- [Apptainer][apptainer] (tested with `apptainer 1.3.6`; not required
-  if you have root permissions on the machine you would like to install
-  _ZARP-cli_ on; in that case, choose one of the `.root.` environment file
-  flavors [below](#3-set-up-environment))
+- Linux (tested with Ubuntu 24.04)
+- [Conda][conda] (tested with `conda 24.11.3`)
+- **Recommended:** [Apptainer][apptainer] (tested with `apptainer 1.3.6`; only
+  required for dependency embedding strategy `APPTAINER`)
 
-> Other versions, especially older ones, are not guaranteed to work.
+!!! warning "Other versions, especially older ones, are not guaranteed to work!"
+
+??? question "How do I install Apptainer?"
+
+    Please follow the [official documentation][apptainer-docs] to install
+    Apptainer (formerly Singularity) globally and configure its permissions.
+    To test whether your Apptainer configuration is adequate, you can check
+    whether the following commands complete without errors:
+
+    ```sh
+    apptainer pull docker://alpine:latest
+    apptainer run alpine_latest.sif echo "Hello from Apptainer"
+    ```
+
+??? tip "Wanna run _ZARP_ on your HPC cluster?"
+
+    _ZARP_ should be able to run on a sufficiently powered (32+GB RAM), modern
+    laptop for most samples. However, if you want to analyze large samples, or
+    a large number of samples, we recommend connecting _ZARP_ to an HPC
+    cluster.
+
+    In that case, you will need to make sure that compatible versions of at
+    least one of Conda and Apptainer (when using dependency embedding
+    strategies `CONDA` and `APPTAINER`, respectively) are installed and
+    properly configured on each machine of the cluster, including the head
+    node(s). Reach out to your systems administrator to set this up for you.
+
+    Once Conda and/or Apptainer are set up, follow the [_ZARP_
+    documentation][zarp-docs] to use, create or extend the necessary
+    Snakemake execution [profiles][snakemake-profiles] to connect _ZARP_
+    runs to your HPC cluster.
 
 ## Installation steps
 
-### 1. Clone ZARP
+### 1. Clone _ZARP_
 
-Clone the [ZARP workflow repository][zarp] with:
+Clone the [_ZARP_ workflow repository][zarp] with:
 
 ```sh
 git clone git@github.com:zavolanlab/zarp
 # or: git clone https://github.com/zavolanlab/zarp.git
 ```
 
-### 2. Clone ZARP-cli
+### 2. Clone _ZARP-cli_
 
-Clone the [ZARP-cli repository][zarp-cli] and traverse into it with:
+Clone the [_ZARP-cli_ repository][zarp-cli] and traverse into it with:
 
 ```sh
 git clone git@github.com:zavolanlab/zarp-cli.git
@@ -40,21 +67,20 @@ cd zarp-cli
 ### 3. Set up environment
 
 In the next step, you need to install the app with its dependencies. For that
-purpose, there exist four different environment files. Use this decision matrix
-to pick the most suitable one for you:
+purpose, there exist two different "environment files". Use this decision
+matrix to pick the most suitable one for you:
 
-| I have root privileges on the machine | I want to run pre-packaged tests | Environment file to use              |
-|:---:|:---:| --- |
-| | | `install/environment.yml` |
-| :check_mark: | | `install/environment.root.yml` |
-| | :check_mark: | `install/environment.dev.yml` |
-| :check_mark: | :check_mark: | `install/environment.dev.root.yml` |
+| I want to run pre-packaged tests | Environment file to use 
+             |
+|:---:| --- |
+| | `install/environment.yml` |
+| :check_mark: | `install/environment.dev.yml` |
 
 To set up the environment, execute the call below, but do not forget to replace
 the placeholder `ENVIRONMENT` with the appropriate file from the table above:
 
 ```sh
-mamba env create -f ENVIRONMENT
+conda env create -f ENVIRONMENT
 ```
 
 ### 4. Activate environment

docs/includes/abbreviations.md

@@ -1 +1,2 @@
 *[CLI]: command-line interface
+*[HPC]: High-Performance Computing

docs/includes/references.md

@@ -1,4 +1,5 @@
 [apptainer]: <https://apptainer.org/>
+[apptainer-docs]: <https://apptainer.org/documentation/>
 [bioanalyzer]: <https://www.agilent.com/en/product/automated-electrophoresis/bioanalyzer-systems>
 [conda]: <https://docs.conda.io/projects/conda/en/latest/index.html>
 [contact]: <mailto:zavolab-biozentrum@unibas.ch>
@@ -8,7 +9,6 @@
 [github-signup]: <https://github.com/signup>
 [htsinfer]: <https://github.com/zavolanlab/htsinfer> 
 [kallisto]: <https://github.com/pachterlab/kallisto>
-[mamba]: <https://github.com/mamba-org/mamba>
 [salmon]: <https://github.com/COMBINE-lab/salmon>
 [snakemake]: <https://github.com/snakemake/snakemake>
 [snakemake-profiles]: <https://snakemake.readthedocs.io/en/stable/executing/cli.html#profiles>
@@ -17,6 +17,7 @@
 [zarp]: <https://github.com/zavolanlab/zarp>
 [zarp-cli]: <https://github.com/zavolanlab/zarp-cli>
 [zarp-cli-issue-tracker]: <https://github.com/zavolanlab/zarp-cli/issues>
+[zarp-docs]: <https://zavolanlab.github.io/zarp/>
 [zarp-issue-tracker]: <https://github.com/zavolanlab/zarp/issues>
 [zarp-qa]: <https://github.com/zavolanlab/zarp/discussions>
 [zarp-supplementary]: <https://zenodo.org/records/10797372.