eDNA-training-24 by LearnerWorld

This training is design for helping first starter in Bioinformatics using the pipeline demo from nf-core

Before you start you can see the pipeline there nextflow/demo

Note if the pipeline demo does not exist just learn the way to run a small pipeline

follow these steps to run the pipeline

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I. install Ubuntu WSL on windows

1. Open powershell ⤴️ on admin mode
2. run

   wsl --install

3. verify that the installation is done with

    wsl --list --verbose

4. clic on windows 🪟 and look for Ubuntu At this step if Ubuntu not run check if your virtual system is active on windows or install it on a virtual environement

II. install conda

a. on WSL

1. Open Ubuntu and run

mkdir -p ~/miniconda3

wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda3/miniconda.sh

bash ~/miniconda3/miniconda.sh -b -u -p ~/miniconda3
rm ~/miniconda3/miniconda.sh

2. After the installation close and open Ubuntu or run

source ~/miniconda3/bin/activate

conda --version

b. on macOS

1. Install Homebrew

/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"

2. install Miniconda

   brew install --cask miniconda

   
   
3. add Miniconda path

   echo 'export PATH="/usr/local/miniconda3/bin:$PATH"' >> ~/.zshrc
   source ~/.zshrc

   
   
4. check installation

   conda --version

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III. install your working environment

1. download the working directory

wget https://github.com/Bboy010/eDNA-training-24/archive/refs/heads/main.zip

2. unzip the folder

sudo apt install unzip

unzip main.zip
rm –r  main.zip

3. create Conda environment

cd eDNA-training-24-main

cd config/

conda env create -f eDNA-training-24.yml

conda activate eDNA-training-24
conda init

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IV. Install Nextflow with Conda

1. Nextflow installation

sudo apt update && sudo apt upgrade -y
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge

conda install -c bioconda nextflow

2. Create and activate the nextflow environment

conda create --name nextflow nextflow

conda activate nextflow

3. Check the installation

nextflow info

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V. Run the pipeline

1. Check the working space available

sudo apt install htop
htop

2. Adjust configuration file if necessary

cd eDNA-training-24-main

vi config/custom.config

3. Make run_pipeline.sh executable

chmod +x run_pipeline.sh 

4. Activate nextflow then launch the pipeline

conda activate nextflow

bash run_pipeline.sh

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