Apptainer_Qiime2_NRCan.recipe

Bootstrap: docker
From: quay.io/qiime2/core:2023.9

%files
    /usr/local/share/ca-certificates/NRCAN-Root-2019-B64.crt /usr/local/share/ca-certificates/NRCAN-Root-2019-B64.crt

%labels
    Qiime2_Author Bolyen,Evan et al
    NRCan_Image_Maintainer Patrick Gagne
    Maintainer_Email patrick.gagne@nrcan-rncan.gc.ca

%help
    This container is a standardised setup for Qiime2
    It includes various programs needed at NRCan

%environment
    # DO NOT OVERRIDE THIS, USE BINDING IN APPTAINER COMMAND INSTEAD ( -B /path/to/temp:/tmp )
    export TMPDIR=/tmp 

%post
    apt update --allow-releaseinfo-change
    apt install -y --no-install-recommends software-properties-common apt-utils
    apt update
    apt install -y --no-install-recommends \
    ca-certificates \
    nano \
    git \
    build-essential \
    zlib1g \
    zlib1g-dev \
    less

    # Install FUNGuild (Patrick Gagne's version for Q2Pipe)
    mkdir /download
    cd /download
    git clone https://github.com/Patg13/FUNGuild.git
    cd FUNGuild
    cp Guilds_v1.1.py /usr/bin
    chmod 755 /usr/bin/Guilds_v1.1.py
    cd /
    rm -rf /download

    # Install Q2Pipe Dependencies (from NRCan/Q2Pipe public repo)
    mkdir /download
    cd /download
    #git clone https://github.com/Patg13/Q2Pipe_Deps.git
    #cd Q2Pipe_Deps
    git clone https://github.com/NRCan/Q2Pipe.git
    cd Q2Pipe/Dependencies
    cp ASV_Table_DNA_Merger.py /usr/bin
    chmod 755 /usr/bin/ASV_Table_DNA_Merger.py 
    cd /
    rm -rf /download
    
    #Install Figaro (Trimming value assessment software)
    cd /opt
    #git clone https://github.com/Zymo-Research/figaro.git
    git clone https://github.com/Patg13/figaro.git
    chmod 755 figaro -R
    cd /opt/figaro
    # Figaro requirements already met by Qiime setup
    pip3 install -r requirements.txt
    sed -i '1i #!/usr/bin/env python3' /opt/figaro/figaro/figaro.py
    ln -s /opt/figaro/figaro/figaro.py /usr/bin/figaro

    #Install Falco MTT (quality assessment tool) stable release (forked from smithlabcode/falco)
    cd /opt
    #git clone https://github.com/Patg13/falco.git
    falco_version=1.2.2_MTT
    #wget --no-check-certificate https://github.com/smithlabcode/falco/releases/download/v1.2.1/falco-"$falco_version"
    wget --no-check-certificate https://github.com/Patg13/falco/releases/download/"$falco_version"/falco-"$falco_version".tar.gz
    tar -zxvf falco-"$falco_version".tar.gz
    cd falco
    ./configure CXXFLAGS="-O3 -Wall"
    make all
    make install
    # Adjust the default limits file to make it more appropriate for metabarcoding analysis
    cd Configuration
    analysis="duplication:1 kmer:1 n_content:0 overrepresented:1 quality_base:0 sequence:1 gc_sequence:1 quality_sequence:0 tile:0 sequence_length:0 adapter:0"
    for i in $analysis
    do
        var=$( echo $i | awk -F':' '{ print $1 }' )
        choice=$( echo $i | awk -F':' '{ print $2 }' )
        line=$( grep -wn "^$var" limits.txt | grep "ignore" | awk -F':' '{ print $1 }' )

        if [ $choice -eq 0 ]
        then
            sed -i ""$line"s/1/0/" limits.txt
        fi
        if [ $choice -eq 1 ]
        then
            sed -i ""$line"s/0/1/" limits.txt
        fi
    done

    # NRCan Certificate Cleanup 
    rm /usr/local/share/ca-certificates/NRCAN-Root-2019-B64.crt
    update-ca-certificates

%runscript
    qiime --info