Commit b3b68b0e authored by Nicolas Elie's avatar Nicolas Elie
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Installation

parent 8497b536

README.md

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@@ -24,12 +24,30 @@ The project is mainly based on the Stardist method: https://github.com/stardist/ 


The proposed installation uses Conda environment: https://docs.conda.io/en/latest/.



1. Install conda

2. Download project : 



1. Require java on your system

Install the JRE on Debian (java)



> sudo apt install default-jre





2. CONDA: Installation on Linux

> https://conda.io/projects/conda/en/latest/user-guide/install/linux.html



wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh

chmod +x Miniconda3-latest-Linux-x86_64.sh

bash Miniconda3-latest-Linux-x86_64.sh -p $HOME/miniconda3



$HOME you can indicate your directory



Close your terminal  



3. Download project : 

> git clone https://git.unicaen.fr/nicolas.elie/redpol-open.git (~ 2.5 Go)

3. cd redpol-open/

4. You can install an environment via the provided environment file(s): installationEnv.yml.

> <span dir="">conda env create -f</span> installationEnv.yml

4. cd redpol-open/

5. You can install an environment via the provided environment file(s): installationEnv.yml.



> conda env create -f requirements.yml





# Procedure

requirements.yml

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name: redpol

channels:

  - defaults

  - nvidia

dependencies:

  - python=3.8

  - cudatoolkit=11.0.*

  - cudnn=8.0.*

  - pillow

  - opencv

  - pandas

  - scipy

  - scikit-image

  - jupyter

  - pip

  - pip:

    - tensorflow==2.4.*

    - csbdeep

    - stardist    

    - shapely

    - python-javabridge

    - python-bioformats

    - geojson