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# How to build our Singularity container
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For now, this Singularity image allows to run the analysis from raw data to taxonomic affiliation of reads.
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# How to build metagWGS Singularity containers
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**Singularity installation**
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... | ... | @@ -8,37 +6,30 @@ Follow instructions on: |
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`https://github.com/sylabs/singularity/blob/master/INSTALL.md`
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We used Singularity version 3.5.1-rc.2+105-g968a0ea24.
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We used Singularity version 3.5.1.
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**Miniconda installation and configuration**
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**Download recipe and .yml file**
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* metagwgs.sif container
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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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wget https://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/blob/dev/env/Singularity_recipe_metagWGS
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wget https://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/blob/dev/env/metagWGS.yml
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```
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**Create conda environment and export it in .yml file**
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* eggnogmapper.sif container
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```
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conda create -n env_metagWGS_december -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
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conda activate env_metagWGS_december
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conda deactivate
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conda env export -n env_metagWGS_december > env_metagWGS_december.yml
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wget https://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/blob/dev/env/Singularity_recipe_eggnog_mapper
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wget https://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/blob/dev/env/eggnog_mapper.yml
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```
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`env_metagWGS_december.yml` has been modified (remove prefix line at the end, remove built of tools, change name at the first line) and the .yml file used for building our Singularity image is [`metagWGS_dependancies.yml`](https://forgemia.inra.fr/genotoul-bioinfo/metagwgs/blob/dev/env/metagWGS_dependancies.yml).
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**Create Singularity recipe**
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Our Singularity recipe is available here: [`Singularity_recipe_metagWGS_dependancies`](https://forgemia.inra.fr/genotoul-bioinfo/metagwgs/blob/dev/env/Singularity_recipe_metagWGS_dependancies).
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**Build Singularity container**
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* metagwgs.sif container
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```
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sudo singularity build metagWGS_with_dependancies.img Singularity_recipe_metagWGS_dependancies
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sudo singularity build metagWGS.sif Singularity_recipe_metagWGS
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```
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* eggnogmapper.sif container
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```
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sudo singularity build eggnog_mapper.sif Singularity_recipe_eggnog_mapper
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``` |