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installation.sh
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installation.sh
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#!/bin/bash -i
directory=$1
## BCALM
echo "####"
echo " "
echo "Installation des paquets essentiels"
echo " "
echo " "
sudo apt -y install make
sudo apt-get -y install build-essential
sudo apt -y install zlib1g-dev
sudo apt -y install git
sudo apt -y install cmake g++
### INSTALLATION de edirect
cd
home=$(pwd)
if ! which conda &> /dev/null; then
# Si Conda n'est pas installé, télécharger et installer Miniconda
echo "####"
echo " "
echo "Installation de Conda"
echo " "
echo " "
cd "$HOME"
mkdir -p miniconda3
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda3/miniconda.sh
bash miniconda3/miniconda.sh -b -u -p miniconda3
echo 'export PATH='$home'/miniconda3/bin:$PATH' >> ~/.bashrc
source ~/.bashrc
fi
# Initialiser Conda
conda init bash
source ~/.bashrc
## INSTALLATION de CONDA
echo "####"
echo " "
echo "Installation de Esearch NCBI"
echo " "
echo " "
cd
sudo apt-get -y update
sudo apt -y install ncbi-entrez-direct
echo 'yes' | sh -c "$(curl -fsSL https://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/install-edirect.sh)"
echo 'export PATH="'$home'/edirect:$PATH"' >> ~/.bashrc
cd
source ~/.bashrc
echo "####"
echo " "
echo "Installation de mamba et création de l'environnement conda de snakemake"
echo " "
conda install -n base -c conda-forge -y mamba
mamba create -c conda-forge -c bioconda -n snakemake snakemake -y
## Conda environement :
for file in "$directory"/*.yml; do
filename=$(basename -- "$file")
extension="${filename##*.}"
filename="${filename%.*}"
conda env create -f $file
done
conda activate sratoolkit
conda install -y -c bioconda parallel-fastq-dump ##Installing parallel-fatq-dump inside sratoolkit conda environement
conda install -y -c bioconda fastqc
yes | pip install multiqc
conda init
conda deactivate
echo " "
echo "####"
echo " "
echo "REINDEER Installation "
echo " "
echo " "
conda init
conda activate bcalm
cd
sudo apt -y install zlib1g-dev
git clone --recursive https://github.com/kamimrcht/REINDEER.git
cd REINDEER
sh install.sh
cd
mamba init
mamba activate snakemake