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**Miniconda installation and configuration**
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```
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wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
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bash Miniconda3-latest-Linux-x86_64.sh
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conda config --set auto_activate_base false
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conda deactivate
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conda config --add channels bioconda
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|
conda config --add channels conda-forge
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```
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**Create .yml file**
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|
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* For the metagwgs.sif container:
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|
```
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# Creation of conda environment
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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
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# Activation of conda environment
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source activate metagWGS_conda_env
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# Desactivation of conda environment
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|
conda deactivate
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# Export of conda environment into a .yml file
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conda env export -n metagWGS_conda_env > metagWGS.yml
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|
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|
# Remove built of tools into metagWGS.yml
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|
|
cat metagWGS.yml | cut -d "=" -f 1,2 > metagWGS.yml
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|
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# Modify metagWGS.yml: remove prefix line at the end, change name of the environment at the first line --> write metagWGS.
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# Your metagWGS.yml file is ready !
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|
```
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|
* For the eggnogmapper.sif container:
|
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|
```
|
|
|
# Creation of conda environment
|
|
|
conda create -n metagWGS_python -c conda-forge -c bioconda python=3.7
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|
|
|
# Activation of conda environment
|
|
|
source activate metagWGS_python
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|
|
|
# Desactivation of conda environment
|
|
|
conda deactivate
|
|
|
|
|
|
# Export of conda environment into a .yml file
|
|
|
conda env export -n metagWGS_python > eggnog_mapper.yml
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|
|
|
|
|
# Remove built of tools into metagWGS.yml
|
|
|
cat eggnog_mapper.yml | cut -d "=" -f 1,2 > eggnog_mapper.yml
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|
|
|
|
|
# Modify eggnog_mapper.yml: remove prefix line at the end, change name of the environment at the first line --> write eggnog_mapper.
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|
|
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|
# Your eggnog_mapper.yml file is ready !
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|
|
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|
``` |