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You only need Matlab for your local job submission and local job running.
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## Git
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We require git to download our repos. If you would like to use another potentially simpler method you will have work that out on your own.
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### Getting git
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***Unix/Linux/MacOS***
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Git is usually available on Unix/Linux/MacOS by default, if you do not have git please consult your operating system documentation for assistance.
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***Windows***
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If you are using Windows you may use [Git for Windows](https://git-for-windows.github.io/). You may also use a Linux/Unix/Posix compatibility layer such as Windows Subsystem for Linux (WSL) aka Bash on Ubuntu for Windows, Bash on Windows 10, or whatever marketing term they are using this week. Or you may also use `git` as a part of cygwin. We, however, will not support GUI based bash and will provide all documentation for git as it is on Linux.
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## EEGLAB
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We support the newest stable version of EEGLAB, we will also accept
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[Merge Requests](https://git.sharcnet.ca/bucanl_eeglab_extensions/batch_context/merge_requests)
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# Project Directory
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Make a directory to house your project, this directory should be a self contained implementation of your pipeline.
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We have provided a zip that starts you out with all the files we provided based on our experiences with our pipeline as well as the correct folder structure. You must install EEGLAB/Amica/Batch Context yourself.
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Suitable directory names should likely avoid spaces. We will use "tutorial_pipeline" for our example. Unpack the EEGLAB zip into `tutorial_pipeline/dependencies/eeglab`.
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In our example the eeglab folder was `eeglab7_1_3_13b` we changed it to `eeglab`.
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For now on all paths are relative to `tutorial_pipeline`.
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Additionally it is now a good time to make a few more folders. Add
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* `scripts/`
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* `config/`
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* `logs/`
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* `data/1_init`
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* `data/2_preproc`
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Additionally, install [amica](https://sccn.ucsd.edu/~jason/amica_web.html) in `dependencies/eeglab/plugins/amica`.
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If you are using Linux and have the Intel Fortran Compiler, Open MPI and GNU Make you can use
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