Installation

mkdir -p ~/src
cd ~/src

git clone https://github.com/ejhonglab/al_analysis
cd al_analysis

# This will make a conda environment named 'al_analysis'
conda env create -f environment.yml
conda activate al_analysis

For al-analysis

Set the environment variables HONG_NAS and HONG2P_FAST_DATA appropriately:

• $HONG_NAS should contain a directory mb_team directly under it.

  • This mb_team directory should contain raw_data and stimulus_data_files directly under it.

  • You may also set HONG2P_DATA as a folder that contains raw_data and stimulus_data_files directly under it.

• $HONG2P_FAST_DATA should contain a local copy of the data under a raw_data directory, again immediately under it. Analysis intermediates will be saved to a directory analysis_intermediates, which will be created under this directory.

Setting up link to Google sheet with metadata

For the analysis to use the metadata in my Google Sheet Hong lab documents/Tom - odor mixture experiments/pair_grid_data, open the sheet and copy the link to a file called pair_grid_data_gsheet_link.txt in the top-level of this repository.

TODO

Document expectation on this Google Sheet? Make public read-only template and share link?

Running

# (or whatever else you named the environment for this project)
conda activate al_analysis

al-analysis <command line arguments ...>

# To display help message describing how to run and different command line arguments
al-analysis -h

Plots will be created under a directory such as pdf, under the current directory.

Installation notes

Initially tested on Ubuntu 18.04, mostly on 20.04, and also believe it has worked on at least 24.04 (not sure if I've tested 26.04 yet). Some things, like symbolic links, may not work as expected by default on Windows.