fltower 0.1.3a2

Software for cytometry analysis.

FLtower

This Python project uses conda to manage dependencies with an environment.yml file (ensuring a reproducible and easy-to-setup environment).

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1. Prerequisites

Before starting, make sure:

1. Conda is installed on your system. If not, download it via Miniconda.

2. You have access to a terminal or command prompt.

2. Installing the Environment

a) Create the Environment

1. Clone the project repository:

   git clone https://github.com/synthetic-biology-group-cbs-montpellier/FLtower.git
   cd FLtower
   

2. Create the conda environment from the environment.yml file:

   conda env create -f environment.yml
   

3. Activate the environment:

   conda activate fltower
   

4. Install FLtower package:

   pip install -e .
   

3. Usage

With the environment activated (conda activate fltower), you can run FLtower script from your data folder (cd <path>) with just this keyword:

fltower

You can also specify your input data folder and where you want to save outputs:

fltower --input <your/in/data/path> --output <your/output/folder>

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4. Deactivating and Removing the Environment

a) Deactivate the Environment

To deactivate the currently active environment, run:

conda deactivate

b) Remove the Environment

To completely remove the environment:

conda env remove -n my_project_env

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5. Recreating or Updating the Environment

a) Update an Existing Environment

If changes have been made to environment.yml, update the environment:

conda env update -f environment.yml

b) Recreate the Environment

If needed, you can delete and recreate the environment:

1. Remove the existing environment:

   conda env remove -n my_project_env
   

2. Recreate it:

   conda env create -f environment.yml
   

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Support

If you encounter any issues or have questions, open an issue in the GitHub repository.

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Contributor's section

Updating Dependencies

1. Add a New Dependency:

   conda install <package_name>
   

   or, for Python-only dependencies not available in conda:

   pip install <package_name>
   

2. Export the updated environment.yml file:

   conda env export -f environment.yml