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Windows Compatible cwltool means that now you can create and run your workflows
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using cwltool on Windows under a [Docker Container](https://docs.docker.com/docker-for-windows/).
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On Windows, all tools and workflows will be executed inside a linux based Docker
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Container. If a Docker Container is not explicitly provided (using [Docker Requirement](http://www.commonwl.org/v1.0/CommandLineTool.html#DockerRequirement))
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by user, then a minimal, posix compliant Alpine Docker image which has Bash pre
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installed as fallback (Default) [Docker Container](https://github.com/frol/docker-alpine-bash).
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You can also provide your own default Docker Container using the `--default-container` argument.
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### ***Windows Versions Supported***:
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# Windows Compatibility
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cwltool is compatible with Windows. This means that you can create and run CWL
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workflows on Windows. On Windows, all workflows and tools are executed in
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[Docker Containers](https://docs.docker.com/docker-for-windows/). The default
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Docker Container is
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[Alpine with Bash support](https://github.com/frol/docker-alpine-bash). You can
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specify other Docker Containers for your tools and workflows using hints,
Here`-j`arg is used to run multiple tests in parallel.
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The`-j`options is used to run multiple tests in parallel.
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## Troubleshooting
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> #### Installing cwltool on Windows is smooth but you may face some problems in setting up Docker. Some of the common issues and their solution are mentioned below.
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You may encounter some problems with Docker on Windows.
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### Docker doesn't work on Windows, even outside cwltool
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**Docker doesn't work on Windows, even outside cwltool.**
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Make sure you followed all instructions carefully while installing Docker. Please
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check the Environment variables. If the problem persists, we recommend consulting
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the [online Docker Community](https://forums.docker.com/).
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Make sure you followed all instructions carefully while installing Docker.
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Please check the Environment variables. If the problem persists, we recommend
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consulting the [online Docker Community](https://forums.docker.com/).
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**Your local drives are not being shared with Docker Container.**
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***On native Docker for Windows (supported by Windows 10):**
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On your tray, next to your clock, right-click on Docker, then click on Settings,
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there you'll find the shared rives: Here you can share your drives with Docker.
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If you encounter a problem with your firewall, please [refer this post](https://blog.olandese.nl/2017/05/03/solve-docker-for-windows-error-a-firewall-is-blocking-file-sharing-between-windows-and-the-containers/).
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### Your local drives are not being shared with Docker Containers
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***On Docker Toolbox:**
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Docker Toolbox uses Virtualbox to create a linux base on which Docker machine runs.
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Your Docker Container will be created inside Virtualbox. To share drives
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in virtualbox, go to **Virtualbox->settings->shared folders->Machine Folders**.
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****On native Docker for Windows (supported by Windows 10):***
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On your tray, next to your clock, right-click on Docker, then click on Settings,
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there you'll find the shared rdives: Here you can share your drives with Docker.
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If you encounter a problem with your firewall, please
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[refer this to post](https://blog.olandese.nl/2017/05/03/solve-docker-for-windows-error-a-firewall-is-blocking-file-sharing-between-windows-and-the-containers/).
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****On Docker Toolbox:***
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Docker Toolbox uses Virtualbox to create a linux base on which Docker machine runs.
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Your Docker Container will be created inside Virtualbox. To share drives
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in virtualbox, go to ****Virtualbox->settings->shared folders->Machine Folders****
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Here Map the drives you want to share with your Docker Container.
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If you want to keep these settings permanent (Recommended!), You should mark the
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`make permanent` checkbox or else these settings will be erased every time your
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If you want to keep these settings permanent (Recommended!), You should mark the
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`make permanent` checkbox or else these settings will be erased every time your
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virtualbox closes.
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**In a Docker Container with shared drives, not all files are shown on `ls`.**
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This means your drives/folders are not shared properly. Docker uses caching,
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which may result in not all files and folders being listed on ls.
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In order to solve this problem, make your drive mapping settings permanent (see previous question).
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### In a Docker Container with shared drives, not all files are shown on `ls`
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**Can't create/modify a file in Docker when using cwltool.**
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When folders are shared with Docker Container, they inherit their current file
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access permissions. If you can write to a folder (with your current privileges)
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on your local machine, you should be able to write to that folder inside Docker
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Container also (provided same user initiated Docker). In all it is a file permission issue.
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So to solve this issue, make sure that on your local system, you have write access for the folders
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in which Docker is trying to create/write file.
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This means your drives/folders are not shared properly. Docker uses caching,
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which may result in not all files and folders being listed on ls. In order to
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solve this problem, make your drive mapping settings permanent (see previous
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question).
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**Workflows with Javascript Expressions occasionally give Timeout errors.**
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To evaluate Javascript Expressions, cwltool looks for Nodejs on your system.
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In case Nodejs isn't installed, JS expressions are executed in a Docker Container.
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In order to avoid waiting forever in case error occurs, cwltool times out js
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expression evaluation after a timeout period (by default 20 seconds). You can
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provide a custom timeout period using `--eval-timeout` argument.
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So if you face this error, the best option is to install Nodejs on your local
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system. If you can't then use the `--eval-timeout` argument and set a higher timeout value.
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> #### If you still face some issues setting up and using Docker on Windows, please consult the online Docker Community. If the problem is specific to cwltool, create an [issue on cwltool](https://github.com/common-workflow-language/cwltool/issues).
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### Can't create/modify a file in Docker when using cwltool
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When folders are shared with Docker Container, they inherit their current file
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access permissions. If you can write to a folder (with your current privileges)
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on your local machine, you should be able to write to that folder inside Docker
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Container also (provided same user initiated Docker). In all it is a file
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permission issue.
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### Workflows with Javascript Expressions occasionally give Timeout errors
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To evaluate Javascript Expressions, cwltool looks for Nodejs on your system.
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In case Nodejs isn't installed, JS expressions are executed in a Docker Container.
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In order to avoid waiting forever in case error occurs, cwltool times out js
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expression evaluation after a timeout period (by default 20 seconds). You can
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provide a custom timeout period using `--eval-timeout` argument. So if you face
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this error, the best option is to install Nodejs on your local system. If you
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can't then use the `--eval-timeout` argument and set a higher timeout value.
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*If you still have problems with setting up and using Docker on Windows, please
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consult the online Docker Community. If the problem is specific to cwltool,
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create an [issue on cwltool](https://github.com/common-workflow-language/cwltool/issues).*
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