Singularity.def

Bootstrap: docker                                                                                                                                                                    
From: ubuntu:latest                                                                                                                                                                  
                                                                                                                                                                                     
%environment
    source /opt/software/conda/bin/activate /opt/software/conda-env
%post
    apt -y update
    apt -y install -y build-essential wget git automake zlib1g zlib1g-dev pkg-config curl unzip

    mkdir -p /opt/software && cd /opt/software

    cd /opt/software
    curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
    sh ./Miniconda3-latest-Linux-x86_64.sh -p /opt/software/conda -b
       
    /opt/software/conda/bin/conda config --add channels bioconda
    /opt/software/conda/bin/conda config --add channels conda-forge

    /opt/software/conda/bin/conda create -p /opt/software/conda-env -y fastp bbmap fastqc spades quast barrnap blast trinity=2.15.1 cd-hit transdecoder diamond kraken2 minimap2 samtools hisat2 qualimap seqtk
    /opt/software/conda/bin/conda clean --all --yes

    wget https://github.com/DaehwanKimLab/centrifuge/archive/refs/tags/v1.0.4.zip
    unzip v1.0.4.zip
    rm v1.0.4.zip

    cd centrifuge-1.0.4
    make
    make install prefix=/usr/
    cd ../