diff --git a/src/content/docs/cwl/cwl-runner-installation.mdx b/src/content/docs/cwl/cwl-runner-installation.mdx
index 6859f47c7..5c1f7d181 100644
--- a/src/content/docs/cwl/cwl-runner-installation.mdx
+++ b/src/content/docs/cwl/cwl-runner-installation.mdx
@@ -3,15 +3,20 @@ title: "CWL Runner Installation"
lastUpdated: 2024-01-18
authors:
- caro-ott
+ - dominik-brilhaus
sidebar:
order: 2
---
-The recommended CWL runner is [cwltool](https://github.com/common-workflow-language/cwltool), the reference implementation for the CWL standards.
-
import { Steps } from '@astrojs/starlight/components';
import { Tabs, TabItem } from '@astrojs/starlight/components';
+The recommended CWL runner is [cwltool](https://github.com/common-workflow-language/cwltool), the reference implementation for the CWL standards.
+
+:::tip
+- Please explore the [cwltool docs](https://cwltool.readthedocs.io/en/latest/) for latest installation instructions.
+- We also recommend to install a software container engine (e.g. [Docker](https://docs.docker.com/engine/install/) or [Podman](https://podman.io/getting-started/installation)).
+:::
@@ -41,11 +46,6 @@ The installation on Windows can be done following the guide [here](https://cwlto
-{/*
-
-
- */}
-
For installation on Linux (Debian/Ubuntu):
@@ -53,7 +53,7 @@ For installation on Linux (Debian/Ubuntu):
1. Run `sudo apt-get update`
-2. Install Python 3 if it is not already preinstalled `sudo apt install python3`
+2. Install Python 3 if it is not already installed `sudo apt install python3`
3. Install python virtual environment `sudo apt install python3.[your version here]-venv`
4. Create a virtual environment `python3 -m venv env` (named env here, name can vary)
5. Activate the virtual environment `source env/bin/activate`
@@ -63,6 +63,15 @@ For installation on Linux (Debian/Ubuntu):
+
+
+
+1. Install [conda-forge](https://conda-forge.org/)
+2. Install cwltool via `conda install -c conda-forge cwltool`
+
+
+
+
@@ -70,9 +79,62 @@ For installation on Linux (Debian/Ubuntu):
- If you are on Windows, start the WSL
- Activate the virtual environment `source env/bin/activate`
-- Navigate to the results destination directory
- Run `cwltool` by specifying the CWL `Workflow` or `CommandLineTool` description file path and the (optional) inputs file path (you can use relative or full paths):
```bash
cwltool path/to/cwlfile.cwl path/to/jobfile.yml
```
+
+### Minimal example
+
+Here is a very simplified example to check, that your cwltool installation functions
+
+
+
+1. Store the following as `echo-tool.cwl`
+
+ ```yaml
+ #!/usr/bin/env cwl-runner
+
+ cwlVersion: v1.2
+
+ class: CommandLineTool
+
+ baseCommand: [echo]
+
+ stdout: message.txt
+
+ inputs:
+ message:
+ type: string
+ inputBinding:
+ position: 1
+
+ outputs:
+ output:
+ type: stdout
+ ```
+
+2. In the same folder, store the following as `job.yml`
+
+ ```yaml
+ message: "I love ARCs and CWL"
+ ```
+
+3. Now you can execute the tool
+ - providing an `input` directly via CLI:
+
+ ```
+ cwltool echo-tool.cwl --message "ARCs are great"
+ ```
+ or
+
+ - providing the `input` via the `job.yml`:
+
+ ```
+ cwltool echo-tool.cwl job.yml
+ ```
+
+4. Both create an `output` file called `message.txt` with your specified message.
+
+