Singularity.WGpipeline

Bootstrap: shub
From: drneavin/SingularityBaseImages:r363_python368
%environment
    export PATH=/opt/DoubletDetection/:/opt/popscle/bin/:/opt:/usr/games:/opt/bedtools2/bin:/opt/conda/envs/py36/bin:/opt/souporcell:/opt/souporcell/troublet/target/release:/opt/conda/bin:/opt/minimap2-2.7:/root/.cargo/bin:/opt/vartrix-v1.1.3-x86_64-linux/:/opt/freebayes/scripts:/opt/freebayes:/opt/vcflib/bin:/opt/vcflib/scripts:$PATH
    export PYTHONPATH=/opt/conda/envs/py36/lib/python3.6/site-packages/
    export LC_ALL=C 
    alias python=python3

%post 
    #!/bin/bash
    eval "$(command conda 'shell.bash' 'hook' 2> /dev/null)"
    export PATH=/opt/conda/bin/:$PATH
    apt update
    yes | apt upgrade

	ldconfig

    mkdir -p /usr/share/man/man1
	yes | apt-get install -y python3-tk
    apt-get install -y openjdk-11-jdk
    java -version


    cd /opt
        git clone https://github.com/broadinstitute/picard.git
        cd picard/
        ./gradlew shadowJar

    cd /opt
        wget https://www.dropbox.com/s/m8u61jn4i1mcktp/TestData4PipelineSmall.tar.gz

    cd /opt
    git clone https://github.com/JonathanShor/DoubletDetection.git
    cd DoubletDetection
    /opt/conda/envs/py36/bin/pip install .

    cd /opt
    wget https://github.com/lh3/minimap2/archive/v2.7.tar.gz
        tar -xzvf v2.7.tar.gz
        cd minimap2-2.7
        make

    cd /opt
    wget https://github.com/arq5x/bedtools2/releases/download/v2.28.0/bedtools-2.28.0.tar.gz
        tar -zxvf bedtools-2.28.0.tar.gz
        cd bedtools2
        make

    cd /opt
    CARGO_HOME=/opt/.cargo RUSTUP_HOME=/opt/.cargo bash -c 'curl https://sh.rustup.rs -sSf | sh -s -- -y'
        . /opt/.cargo/env
        which cargo
        rustup default stable
        yes | apt-get install git

    cd /opt
        git clone https://github.com/wheaton5/souporcell.git
            cd souporcell/troublet
            cargo build --release
            cd /opt/souporcell/souporcell
            cargo build --release
    cd /opt
        wget https://github.com/10XGenomics/vartrix/releases/download/v1.1.3/vartrix-v1.1.3-x86_64-linux.tar.gz
            tar xzvf vartrix-v1.1.3-x86_64-linux.tar.gz
            rm vartrix-v1.1.3-x86_64-linux.tar.gz
            export PATH=/opt/vartrix-v1.1.3-x86_64-linux:$PATH

    cd /opt
    wget https://github.com/samtools/htslib/releases/download/1.10.2/htslib-1.10.2.tar.bz2
        tar xvfj htslib-1.10.2.tar.bz2
        cd htslib-1.10.2
        ./configure
        make
        make install

    cd /opt
        git clone --single-branch --branch v1.0.0 https://github.com/sc-eQTLgen-consortium/WG1-pipeline-QC.git

    cd /opt
        wget https://github.com/samtools/samtools/releases/download/1.10/samtools-1.10.tar.bz2
        tar xvfj samtools-1.10.tar.bz2
        rm samtools-1.10.tar.bz2
        cd samtools-1.10
        ./configure
        make
        make install

    cd /opt
        wget https://github.com/samtools/bcftools/releases/download/1.10.2/bcftools-1.10.2.tar.bz2
        tar xvfj bcftools-1.10.2.tar.bz2
        rm bcftools-1.10.2.tar.bz2
        cd bcftools-1.10.2
        ./configure
        make
        make install


    cd /opt
    git clone https://github.com/ekg/freebayes.git
    wget https://github.com/ekg/freebayes/releases/download/v1.3.1/freebayes-v1.3.1
        mv freebayes-v1.3.1 freebayes/freebayes
        chmod 777 freebayes/freebayes

    cd /opt
    wget http://ftp.gnu.org/gnu/parallel/parallel-latest.tar.bz2
        tar xjf parallel-latest.tar.bz2
        cd parallel-*
        ./configure && make
        yes | make install


    cd /opt
    git clone https://github.com/statgen/popscle.git
        cd popscle
        # sed -i 's/set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O3 -pthread")/set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O3 -pthread --std=c++11")/g' CMakeLists.txt
        cat CMakeLists.txt
        mkdir build
        cd build
        cmake ..
        make
    echo 'alias popscle=/opt/popscle/bin/popscle' >> $SINGULARITY_ENVIRONMENT


    sed -i 's/louvain.set_rng_seed(random_state)/partition_kwargs["seed"] = random_state/g'  /opt/conda/envs/py36/lib/python3.6/site-packages/scanpy/tools/_louvain.py

##############################
# setup scripts for users
##############################
%apphelp setup
    This function copies pipeline scripts to the user systems from the Singularity image.
%appenv setup
    SCRIPT_DIR=/opt/WG1-pipeline-QC/Demultiplexing
    export SCRIPT_DIR
%apprun setup
    exec cp -a ${SCRIPT_DIR}/. "$PWD"

%apphelp test_dataset
    This function copies the yaml scripts to the user systems from the Singularity image.
%appenv test_dataset
    TAR=/opt/TestData4PipelineSmall.tar.gz
    export TAR
%apprun test_dataset
    exec cp -a ${TAR} "$@"



%labels 
    Authors Drew Neavin and Anne Senabouth
	Image_version = 1.0.0