Skip to content
This repository has been archived by the owner on Dec 10, 2021. It is now read-only.

Latest commit

 

History

History
80 lines (55 loc) · 2.76 KB

start-web-server.md

File metadata and controls

80 lines (55 loc) · 2.76 KB
Raw

labbox-ephys web server

Tested on Linux, should also run on macOS and Windows Subsystem for Linux.

Prerequisites and kachery setup

It is recommended that you start with a fresh conda environment with Python 3.8 or higher. For example:

conda create -n labbox-ephys python=3.8

After activating the new environment (conda activate labbox-ephys), install the following prerequisite packages:

conda install -c conda-forge nodejs
npm install -g serve
pip install labbox-ephys

# On macOS you may need to use the following to get a recent version of nodejs:
# conda install nodejs -c conda-forge --repodata-fn=repodata.json

Choose an existing directory where temporary kachery files will be stored and set the KACHERY_STORAGE_DIR environment variable (if not set, $HOME/kachery-storage will be used):

# This should be the full path to an existing directory.
# For example, you could use: $HOME/kachery-storage
export KACHERY_STORAGE_DIR="<your-chosen-tmp-file-directory>"

Ensure that this environment variable is set with each new terminal session by adding the above line to your ~/.bashrc file.

Open a new terminal and start a kachery-p2p daemon, selecting a <node-label> for display purposes:

# Make sure you are in the conda environment created above
# and that the KACHERY_STORAGE_DIR env variable is set
kachery-p2p-start-daemon --label <node-label>

Keep this running. It allows communication between the Python script and the GUI. See below for more advanced configuration options, or see kachery-p2p.

Installing and running the app

Upgrade to the latest labbox-ephys (it may be worth restarting the kachery daemon in case updates have been made to the kachery-p2p package):

pip install --upgrade labbox-ephys

Now run the labbox-ephys service:

# First make sure you are in the conda environment
labbox-ephys

Open the web app in a browser at http://localhost:15351.

On the first run, this should display an empty workspace with instructions on importing recordings and sortings.

Advanced kachery daemon configuration

You can also set the following optional environment variables

# KACHERY_P2P_CONFIG_DIR
# This should correspond to the config directory being used by the kachery-p2p daemon
# By default it is $HOME/.kachery-p2p
export KACHERY_P2P_CONFIG_DIR="<Config directory for kachery-p2p>"

# KACHERY_P2P_API_PORT
# This should correspond to the port being used by the kachery-p2p daemon
# By default it is 15351
export KACHERY_P2P_API_PORT="<Port number used by kachery-p2p daemon>"

See kachery-p2p