Installation

This page details the install instructions for WIPAR.

Requirements

WIPAR supports Windows and Linux distributions. First, you need to install a Conda-based Python3 distribution like Anaconda. Then follow the install instructions for Snakemake.

Installation

Currently WIPAR is only available on Github, so you need to clone the repository to a folder of your choice. This folder will from now on be referenced as /WIPAR.

$ git clone https://github.com/michaelschaub/calcium-imaging-analysis.git

You should have the following file structure in your /WIPAR folder.

.
├── config (▶)     | config files for pipeline runs
├── resources (▶)  | experimental data and brain atlases
├── ci_lib (🛠)     | python package containing all custom functions for the pipeline steps
├── workflow (🛠)   | Snakemake logic like rules, envs and entry scripts
└── SLURM           | batch files to run on computational clusters

(▶) Running & configuring pipeline (for User)
(🛠) Extending pipeline functions (for Developers)

Experimental Data

To run WIPAR you first need to provide the experimental data you want to process into the /WIPAR/resources/experiment/ folder in the following way

├── ...
├── resources
│   ├── meta
│   └── experiment
│       ├── subject1
│       │   ├── experiment_id1
│       │   ├── experiment_id2
│       │   └── ...
│       ├── subject2
│       │   ├── experiment_id1
│       │   ├── experiment_id2
│       │   └── ...
│       └── ...
├── ...

Each datasets is in a separate folder for each subject and each experiment_id (usual the time and date). A concrete example for the path of a single dataset is /WIPAR/resources/experiment/GN06/2021-01-20_10-15-16.

Now you can test your installation with the example from the tutorial.

Note

If you encounter problems during the setup, please have a look at the trouble shooting