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update setup #134

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Dec 7, 2022
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update setup #134

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8 changes: 4 additions & 4 deletions setup.md
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Expand Up @@ -30,7 +30,7 @@ data-toggle="tab">Linux</a></li>
2. [Open Benten in the marketplace](https://marketplace.visualstudio.com/items?itemName=sbg-rabix.benten-cwl){:target="_blank"}{:rel="noopener noreferrer"} and click the `Install` button or follow the directions.

3. Install and configure Windows Subsystem for Linux 2 (WSL2), and Docker Desktop
1. Confirm that you are running Windows 10, version 2004 or higher (Build 19041 and higher) or Windows 11.
1. Confirm that you are running Windows 10, version 1903 or higher (Build 18362 and higher) or Windows 11.

> ## Check your Windows version
> To check your Windows version and build number, press the Windows logo key + <kbd>R</kbd>, type `winver`, select OK.
Expand Down Expand Up @@ -104,7 +104,7 @@ data-toggle="tab">Linux</a></li>

1. Download and install [VSCode](https://code.visualstudio.com/){:target="_blank"}{:rel="noopener noreferrer"}.
2. [Open Benten in the marketplace](https://marketplace.visualstudio.com/items?itemName=sbg-rabix.benten-cwl){:target="_blank"}{:rel="noopener noreferrer"} and click the `Install` button or follow the directions.
3. [Install docker](https://docs.docker.com/engine/install/){:target="_blank"}{:rel="noopener noreferrer"}
3. [Install docker server](https://docs.docker.com/engine/install/#server){:target="_blank"}{:rel="noopener noreferrer"}
4. [Enable docker usage as a non-root user](https://docs.docker.com/engine/install/linux-postinstall/#manage-docker-as-a-non-root-user){:target="_blank"}{:rel="noopener noreferrer"}
5. Install the latest version of `cwltool`.
1. First we will make a Python virtual environment by running the following commands in the terminal.
Expand Down Expand Up @@ -163,7 +163,7 @@ data-toggle="tab">Linux</a></li>
{: .language-bash}
6. Create a virtual environment using conda
~~~
conda create --name cwltutorial
conda create --name cwltutorial python==3.10 mamba
~~~
{: .language-bash}
7. Activate the virtual environment
Expand All @@ -173,7 +173,7 @@ data-toggle="tab">Linux</a></li>
{: .language-bash}
8. Install the CWL reference runner (`cwltool`), and some helper programs using conda
~~~
conda install cwltool graphviz wget git nodejs
mamba install cwltool graphviz wget git nodejs
~~~
{: .language-bash}

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