EnriqueDoster/MEG-amrplusplus-RGI-SNPconfirmation:latest

$ singularity pull shub://EnriqueDoster/MEG-amrplusplus-RGI-SNPconfirmation:latest

Singularity Recipe

Bootstrap: docker
From: debian:jessie-slim

#Includes rgi idba trimmomatic bwa samtools bedtools freebayes bbmap vcftools htslib resistomeanalyzer, rarefactionanalyzer, SNPfinder
%environment
    export PATH=/usr/local/envs/compute/bin/:${PATH}
    
%post
    ## Java install doesn't work, but can load java module from summit
    apt update \
    && apt install -y --no-install-recommends \
    build-essential ca-certificates sudo \
    git make automake autoconf wget unzip sed \
    zlib1g-dev curl libbz2-dev locales libncurses5-dev liblzma-dev libcurl4-openssl-dev software-properties-common apt-transport-https\
    libglib2.0-0 libxext6 libsm6 libxrender1 \
    python3-pip python3-docopt python3-pytest python-dev python3-dev\
    libssl-dev zlib1g-dev fonts-texgyre \
    gcc g++ gfortran libblas-dev liblapack-dev dos2unix tabix \
    r-base-core r-recommended hmmer\
    && rm -rf /var/lib/apt/lists/*

    #Installing Anaconda 2 and Conda 4.5.11
    wget -c https://repo.continuum.io/archive/Anaconda2-5.3.0-Linux-x86_64.sh
    sh Anaconda2-5.3.0-Linux-x86_64.sh -bfp /usr/local

    # add bioconda channels
    conda config --add channels defaults
    conda config --add channels conda-forge
    conda config --add channels bioconda
    conda update conda
    conda clean --all --yes
    
    # install bulk of bioinformatic tools using conda 
    conda create -n compute python=3 rgi idba trimmomatic bwa samtools bedtools freebayes bbmap vcftools htslib ncurses    

    # make /data and /scripts so we can mount it to access external resources
    #if [ ! -d /data ]; then mkdir /data; fi
    #if [ ! -d /scripts ]; then mkdir /scripts; fi
    
    . /usr/local/bin/activate compute
        
    # resistomeanalyzer
    cd /usr/local
    git clone https://github.com/cdeanj/resistomeanalyzer.git
    cd resistomeanalyzer
    make
    cp resistome /usr/local/bin
    #ln -s /usr/local/resistomeanalyzer/* /usr/local/bin/
    cd /

    # RarefactionAnalyzer
    cd /usr/local
    git clone https://github.com/cdeanj/RarefactionAnalyzer.git
    cd RarefactionAnalyzer
    make
    cp rarefaction /usr/local/bin
    cd /

    # Install kraken
    cd /usr/local
    git clone https://github.com/DerrickWood/kraken2.git
    cd kraken2/
    ./install_kraken2.sh /usr/local/kraken2
    cp /usr/local/kraken2/kraken2 /usr/local/bin
    cp /usr/local/kraken2/kraken2-build /usr/local/bin
    cp /usr/local/kraken2/kraken2-inspect /usr/local/bin
    cd /
    
    chmod -R 777 /usr/local/
    
%runscript
    echo "Now inside Singularity container woah..."
    exec /bin/bash    
   
%test

Collection

• Name: EnriqueDoster/MEG-amrplusplus-RGI-SNPconfirmation
• License: MIT License

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