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create_conda_envs.sh
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create_conda_envs.sh
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#!/bin/bash -e
#Create a conda_envs directory if not existing
if ! [[ -d ./conda_envs ]]; then
mkdir ./conda_envs
fi
# Define a list of conda envs to create: --> conda_env[env_name]="Tools to install in the env"
declare -A conda_env
conda_env[env-preprocessing]="trim-galore fastp trimmomatic"
conda_env[env-alignment]="bwa bowtie2 samtools"
# Iterate through each of the envs, create it if not already present in the conda_envs directory
for env_name in ${!conda_env[@]}; do
# echo $env_name
if ! [[ -d conda_envs/${env_name} ]]; then
echo "Creating ${env_name}..."
conda_flags="-c bioconda -c conda-forge -c defaults --mkdir --yes --quiet"
conda create ${conda_flags} --prefix conda_envs/${env_name} ${conda_env[${env_name}]}
echo Created ${env_name}.
else
echo "${env_name} already exists, skipping..."
fi
# echo ${conda_env[${env_name}]}
done
# Create MultiQC env from a yml file
if ! [[ -d conda_envs/env-multiQC ]]; then
echo "Create env-MultiQC..."
conda env create --prefix conda_envs/env-multiQC --file env-multiqc.yml --yes --quiet
echo Created env-multiQC.
else
echo "env-multiQC already exists, skipping..."
fi