From 95b236f10c4aff4bac736665c32d910fad75424a Mon Sep 17 00:00:00 2001 From: Dominik Brilhaus Date: Wed, 13 Nov 2024 18:41:18 +0100 Subject: [PATCH 1/2] reorder cwl articles --- src/content/docs/cwl/cwl-examples.md | 2 ++ src/content/docs/cwl/cwl-introduction.md | 4 +++- src/content/docs/cwl/cwl-metadata.md | 2 ++ src/content/docs/cwl/cwl-runner-installation.md | 4 ++-- src/content/docs/cwl/index.mdx | 2 ++ 5 files changed, 11 insertions(+), 3 deletions(-) diff --git a/src/content/docs/cwl/cwl-examples.md b/src/content/docs/cwl/cwl-examples.md index 3f15c6bcd..ebb5f667c 100644 --- a/src/content/docs/cwl/cwl-examples.md +++ b/src/content/docs/cwl/cwl-examples.md @@ -3,6 +3,8 @@ title: "CWL Examples" lastUpdated: 2024-02-05 authors: - caro-ott +sidebar: + order: 4 --- # CWL Examples diff --git a/src/content/docs/cwl/cwl-introduction.md b/src/content/docs/cwl/cwl-introduction.md index cade3a10a..eb5d243a9 100644 --- a/src/content/docs/cwl/cwl-introduction.md +++ b/src/content/docs/cwl/cwl-introduction.md @@ -3,11 +3,13 @@ title: "CWL Introduction" lastUpdated: 2024-01-18 authors: - caro-ott +sidebar: + order: 1 --- # What is CWL? -CWL is short for Common Workflow Language. +CWL is short for **Common Workflow Language**. It is an open standard for describing how to run command line tools and connect them to create workflows, which can then be incorporated in other workflows if needed (nested workflows). Descriptions in CWL are portable across a variety of platforms that support the CWL diff --git a/src/content/docs/cwl/cwl-metadata.md b/src/content/docs/cwl/cwl-metadata.md index 4fb13aab9..73f4aa080 100644 --- a/src/content/docs/cwl/cwl-metadata.md +++ b/src/content/docs/cwl/cwl-metadata.md @@ -3,6 +3,8 @@ title: "CWL Metadata" lastUpdated: 2024-02-05 authors: - caro-ott +sidebar: + order: 3 --- # CWL Metadata diff --git a/src/content/docs/cwl/cwl-runner-installation.md b/src/content/docs/cwl/cwl-runner-installation.md index f1754d262..d785ef640 100644 --- a/src/content/docs/cwl/cwl-runner-installation.md +++ b/src/content/docs/cwl/cwl-runner-installation.md @@ -3,10 +3,10 @@ title: "CWL Runner Installation" lastUpdated: 2024-01-18 authors: - caro-ott +sidebar: + order: 2 --- -# CWL runner installation - The recommended CWL runner is [cwltool](https://github.com/common-workflow-language/cwltool), the reference implementation for the CWL standards. diff --git a/src/content/docs/cwl/index.mdx b/src/content/docs/cwl/index.mdx index ff25a627e..73877e7d1 100644 --- a/src/content/docs/cwl/index.mdx +++ b/src/content/docs/cwl/index.mdx @@ -3,6 +3,8 @@ title: Computational Workflows lastUpdated: 2023-02-05 authors: - kevin-frey +sidebar: + order: 0 --- import { CardGrid } from '@astrojs/starlight/components'; import { LinkCard } from '@astrojs/starlight/components'; From 624fd72f6e7554314d0a515439b403f17c89e29c Mon Sep 17 00:00:00 2001 From: Dominik Brilhaus Date: Wed, 13 Nov 2024 18:48:30 +0100 Subject: [PATCH 2/2] polish cwl installation --- .../docs/cwl/cwl-runner-installation.md | 48 ------------ .../docs/cwl/cwl-runner-installation.mdx | 78 +++++++++++++++++++ 2 files changed, 78 insertions(+), 48 deletions(-) delete mode 100644 src/content/docs/cwl/cwl-runner-installation.md create mode 100644 src/content/docs/cwl/cwl-runner-installation.mdx diff --git a/src/content/docs/cwl/cwl-runner-installation.md b/src/content/docs/cwl/cwl-runner-installation.md deleted file mode 100644 index d785ef640..000000000 --- a/src/content/docs/cwl/cwl-runner-installation.md +++ /dev/null @@ -1,48 +0,0 @@ ---- -title: "CWL Runner Installation" -lastUpdated: 2024-01-18 -authors: - - caro-ott -sidebar: - order: 2 ---- - -The recommended CWL runner is [cwltool](https://github.com/common-workflow-language/cwltool), the -reference implementation for the CWL standards. - -## Installation Windows - -The installation can be done following the guide [here](https://cwltool.readthedocs.io/en/latest/#ms-windows-users). - - - Install Windows Subsystem for Linux from the Microsoft Store - - ![WSL](@images/guides/cwl/wsl.png) - - - Install Debian from the Microsoft Store - - ![Debian](@images/guides/cwl/debian.png) - - Set Debian as your default WSL 2 distro: `wsl --set-default debian` - - Install [Docker Desktop for Windows](https://desktop.docker.com/win/main/amd64/Docker%20Desktop%20Installer.exe) - - Start Docker Desktop and Navigate to Settings - - Select "Use WSL 2 based engine" in the general tab and apply - ![Docker WSL2](@images/guides/cwl/docker-wsl2.png) - - Select "Enable Integration with my default distro" in the resources tab under WSL Integration - ![Docker WSL Integration](@images/guides/cwl/docker-wsl-integration.png) - - Start WSL - - Follow the Instructions for Linux (Debian/Ubuntu) - - ## Installation Linux (Debian/Ubuntu) - - - Run `sudo apt-get update` - - Install Python 3 if it is not already preinstalled `sudo apt install python3` - - Install python virtual environment `sudo apt install python3.[your version here]-venv` - - Create a virtual environment `python3 -m venv env` (named env here, name can vary) - - Activate the virtual environment `source env/bin/activate` - - Install `cwltool` with pip `pip install cwltool` - - ## cwltool usage - - - 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: `cwltool path/to/cwlfile.cwl path/to/jobfile.yml` (you can use relative or full paths) diff --git a/src/content/docs/cwl/cwl-runner-installation.mdx b/src/content/docs/cwl/cwl-runner-installation.mdx new file mode 100644 index 000000000..6859f47c7 --- /dev/null +++ b/src/content/docs/cwl/cwl-runner-installation.mdx @@ -0,0 +1,78 @@ +--- +title: "CWL Runner Installation" +lastUpdated: 2024-01-18 +authors: + - caro-ott +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 installation on Windows can be done following the guide [here](https://cwltool.readthedocs.io/en/latest/#ms-windows-users). + + + +1. Install Windows Subsystem for Linux from the Microsoft Store + + ![WSL](@images/guides/cwl/wsl.png) + +2. Install Debian from the Microsoft Store + + ![Debian](@images/guides/cwl/debian.png) + +3. Set Debian as your default WSL 2 distro: `wsl --set-default debian` +4. Install [Docker Desktop for Windows](https://desktop.docker.com/win/main/amd64/Docker%20Desktop%20Installer.exe) + - Start Docker Desktop and Navigate to Settings + - Select "Use WSL 2 based engine" in the general tab and apply + ![Docker WSL2](@images/guides/cwl/docker-wsl2.png) + - Select "Enable Integration with my default distro" in the resources tab under WSL Integration + ![Docker WSL Integration](@images/guides/cwl/docker-wsl-integration.png) +5. Start WSL +6. Follow the Instructions for Linux (Debian/Ubuntu) + + + + +{/* + + + */} + + + +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` +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` +6. Install `cwltool` with pip `pip install cwltool` + + + + + + + + +## cwltool usage + +- 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 +```