GitLab

1. Miniconda installation and configuration

wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh
conda config --set auto_activate_base false
conda deactivate
conda config --add channels bioconda
conda config --add channels conda-forge

2. Create .yml file

• For the metagwgs.sif container:

# Creation of conda environment
conda create -n metagWGS_conda_env -c conda-forge -c bioconda cutadapt sickle-trim bwa samtools bedtools spades megahit kaiju cd-hit krona subread fastqc prokka bcbio-gff multiqc diamond pandas quast fraggenescan bowtie2 metabat2 busco=3.0.2 cat

# Activation of conda environment
source activate metagWGS_conda_env

# Deactivation of conda environment
conda deactivate

# Export of conda environment into a .yml file
conda env export -n metagWGS_conda_env > metagWGS.yml

# Remove built of tools into metagWGS.yml
cat metagWGS.yml | cut -d "=" -f 1,2 > metagWGS.yml

# Modify metagWGS.yml: remove prefix line at the end, change name of the environment at the first line --> write metagWGS.

# Your metagWGS.yml file is ready !

• For the eggnogmapper.sif container:

# Creation of conda environment
conda create -n metagWGS_python -c conda-forge -c bioconda python=3.7

# Activation of conda environment
source activate metagWGS_python

# Deactivation of conda environment
conda deactivate

# Export of conda environment into a .yml file
conda env export -n metagWGS_python > eggnog_mapper.yml

# Remove built of tools into metagWGS.yml
cat eggnog_mapper.yml | cut -d "=" -f 1,2 > eggnog_mapper.yml

# Modify eggnog_mapper.yml: remove prefix line at the end, change name of the environment at the first line --> write eggnog_mapper.

# Your eggnog_mapper.yml file is ready !