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ibl-instructions.md

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IBL-rig installation

  1. Navigate to C:/

  2. Clone iblrig code:

    git clone https://github.com/int-brain-lab/iblrig

  3. Navigate to ../iblrig:

    cd iblrig

  4. Install ibl package, it will automatically create an enviroment:

    python install.py

  5. When prompted to install Bonsai press y and enter.

  6. Activate the environment created by iblrig:

    conda activate iblenv

  7. You can now launch pybpod (a GUI should appear):

    start-pybpod

Alyx installation

if your machine is running Windows 10 you have to create a Windows subsystem for Linux. For that:

  1. Download and install Ubuntu Terminal on Windows

  2. Then enable and install Windows subsystem. Open a PowerShell as admin and type:

    Enable-WindowsOptionalFeature -Online -FeatureName Microsoft-Windows-Subsystem-Linux

  3. Download Ubuntu 18.04 distro. Double click to run (forget about unzipping)

  4. Add distro to Windows PATH from PowerShell line:

    $userenv = [System.Environment]::GetEnvironmentVariable("Path", "User")
[System.Environment]::SetEnvironmentVariable("PATH", $userenv + ";C:\Users\Administrator\Ubuntu", "User")

  5. Run Ubuntu 18.04 which should appear in the launch line of Windows if you type that. It will install some stuff. If prompted to ask every time for reboot just move to yes with the arrows in the keyboard and press enter. It may reboot a couple of times (so close everything else before this step). You will have to create a user and a sudo password.

  6. Now you should follow the instructions to setup alyx. However don´t do it. Follow the modification of their instructions that I write below. Close any open Ubuntu prompts, launch a new one like in the previous step. Then run:

$ sudo apt-get update
$ sudo apt-get install python3-pip python3-dev libpq-dev postgresql postgresql-contrib virtualenv
$ sudo touch /var/log/alyx.log; sudo chmod 776 /var/log/alyx.log;
$ sudo mkdir uploaded
$ sudo chmod 775 -fR uploaded
$ sudo chown www-data:www-data -fR uploaded
$ git clone https://github.com/cortex-lab/alyx.git
$ cd alyx
$ virtualenv alyxvenv --python=python3
$ source ./alyxvenv/bin/activate
$ pip install -r requirements.txt
$ python setup.py

Now it will ask for a database name, a username and a password like:

Enter a database name [labdb]: Enter a postgres username [labdbuser]: Enter a postgres password:

Wait until is done (do NOT press ctrl C). Finally initialize fixtures:

$ cd scripts
$ ./load-init-fixtures.sh

Wait until is done. Run this to launch the server:

$ python alyx/manage.py runserver

Now open any explorer like Firefox or Chrome and try to reach the server in http://localhost:8000/admin. Use user: admin and password:admin

You should now see something like

snapshot