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**Table of contents**
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[[_TOC_]]
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# Downloading
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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 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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**Running git clone**
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From your command line navigate to the directory you want your project to be in. Git clone will make a folder in your current directory so it is safe to do this in Documents for instance.
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```bash
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cd /path/to/your/directory
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```
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Now clone the repository recursively in order to also get all required submodules.
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```bash
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git clone --recursive https://git.sharcnet.ca/bucanl_pipelines/eeg_pipe_asr_amica.git
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```
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Move (or rename) your directory to your desired project name
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```bash
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mv eeg_pipe_asr_amica my-project
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```
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Change directory to your project
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```bash
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cd my-project
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```
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# Install
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The pipeline is designed to be used to defer computation to cluster of computers. We therefore need to have a copy of all files both locally and on the remote cluster.
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**Data**
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Before setting up the remote cluster machine(s) you should copy your .set or .ess data to your `<project root>/analysis/data/1_init` directory.
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**Practice Data Files**
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There are 10 practice data files that can be downloaded from the following owncloud link if you wish to practice before you obtain your own data:
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* :cloud: [OwnCloud at Westgrid](https://owncloud.westgrid.ca/index.php/s/0Rf5ekmbsEJLW6c)
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The eeg_pipeline_asr_amica requires a setup on the server side in order to be able to run the scripts remotely. The setup is compiled into a script. You may run this script locally but it is not supported on Windows.
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**Synchronize**
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Synchronize your data/pipeline project directory with the remote cluster using `scp` or another method supported by your remote cluster administrators. Secure copy (`scp`) will copy all files over the existing files and therefore wastes time transferring files that already exist on the remote. Systems that support `scp`/`ssh` usually will support `rsync` as well which only sends the differences between your files and the remote files speeding up your transfer. You may also use a visual diff program like `meld` over `sshfs` which is "secure shell file system." For Windows a suitable program for `scp` is [MobaXterm](http://mobaxterm.mobatek.net/). For Unix/Linux & MacOS users you will already have `scp` and you likely will also have `rsync`.
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**Remote requirements**
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The setup script will warn you if you are missing requirements but the basic requirements for remote setup are:
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* `ifort` (Intel C++ and Fortran Compiler)
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* `mpif90` (Open MPI 1.X)
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* `octave` GNU Octave Interpreter (Must be compiled with Java support)
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**Setup Script**
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On the remote, through `ssh` run the script `./setup-remote.sh`
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*on remote server*
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```bash
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cd /path/to/root/of/project
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# chmod +x of the setup-remote.sh script is only required if
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# coming from a file system that is not posix
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chmod +x ./setup-remote.sh
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./setup-remote.sh
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```
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Note: At this point `./setup-remote.sh` will run various tests and scripts to install the proper octave packages and compile amica. Both Octave and Amica frequently need environment variables to be set in order to properly compile and run. You will receive the message
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```
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Prompt:We need to load session environment variables for
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amica
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Prompt:Select a file containing environment variables
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Note:You may need to select a different version based on your scheduler
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File name: [analysis/support/config/amica.sesinit]:
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```
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* If you are using Sharcnet's orca cluster you will want to leave this as the default. (Just press enter)
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* If you are using Compute Canada's Graham or Cedar you will want to use "analysis/support/config/amica-sbatch.sesinit". `./setup-remote.sh` has readline enabled so you may use tab completion for the file names.
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Any problems with setup can be reported in [Issues](https://git.sharcnet.ca/bucanl_pipelines/eeg_pipe_asr_amica/issues)
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***
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[ :arrow_right: **Next Step**](opening-eeglab)
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[ :house: **Return to Main Page**](https://git.sharcnet.ca/bucanl_pipelines/eeg_pipe_asr_amica/wikis/home) |
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\ No newline at end of file |