container files

docs/projectinfo/container_images.rst

@@ -12,13 +12,167 @@ Singularity definition file
 
 .. code-block:: none 
 
-	Testing
+    Bootstrap: docker
+    From: ubuntu:20.04
 
+    %environment
+        PATH=$PATH:/usr/bin:/usr/bin/bcftools-1.16/bin/:/usr/bin/samtools-1.16/bin/:/usr/bin/miniconda3/bin:$PATH
+
+        export PATH
+        export BCFTOOLS_PLUGINS=/usr/bin/bcftools-1.16/plugins/
+
+    %post
+        apt-get -y update
+        apt -y update
+
+        apt install software-properties-common -y
+
+        # Install bwa
+        apt-get install -y wget \
+        bwa \
+        curl \
+        git \
+        tar \
+        build-essential \
+        zlib1g-dev \
+        libbz2-dev \
+        liblzma-dev \
+        libncurses5-dev \
+        unzip
+
+        # build-essential for bcftools1.16
+        # zlib1g-dev for bcftools1.16
+        # libbz2-dev for bcftools1.16
+        # liblzma-dev for bcftools1.16
+        # libncurses5-dev for samtools1.16
+        # unzip for illumina product files
+        # https://www.devmanuals.net/install/ubuntu/ubuntu-20-04-focal-fossa/installing-bwa-on-ubuntu20-04.html
+
+        mkdir -p /usr/share/man/man1/
+        apt-get install -y openjdk-8-jdk
+        apt-get install -y openjdk-8-jre
+        update-alternatives --config java
+        update-alternatives --config javac
+
+        wget -P /usr/bin/ https://github.com/broadinstitute/picard/releases/download/2.27.2/picard.jar
+
+        wget -P /usr/bin/ https://sourceforge.net/projects/samtools/files/samtools/1.16/bcftools-1.16.tar.bz2
+        cd /usr/bin/
+        tar xvfj /usr/bin/bcftools-1.16.tar.bz2
+        cd /usr/bin/bcftools-1.16/
+        ./configure --prefix=/usr/bin/bcftools-1.16
+        make
+        make install
+        export PATH="/usr/bin/bcftools-1.16/bin:$PATH"
+        rm /usr/bin/bcftools-1.16.tar.bz2
+
+        # install samtools
+        wget -P /usr/bin/ https://sourceforge.net/projects/samtools/files/samtools/1.16/samtools-1.16.tar.bz2
+        cd /usr/bin/
+        tar xvfj /usr/bin/samtools-1.16.tar.bz2
+        cd /usr/bin/samtools-1.16/
+        ./configure --prefix=/usr/bin/samtools-1.16
+        make
+        make install
+        export PATH="/usr/bin/samtools-1.16/bin:$PATH"
+        rm /usr/bin/samtools-1.16.tar.bz2
+
+        wget -P /usr/bin/bcftools-1.16/plugins/ https://software.broadinstitute.org/software/gtc2vcf/gtc2vcf_1.16-20221221.zip
+        cd /usr/bin/bcftools-1.16/plugins/
+        unzip gtc2vcf_1.16-20221221.zip
+
+        # Install miniconda 
+        wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
+        bash Miniconda3-latest-Linux-x86_64.sh -b -f -p /usr/bin/miniconda3/
+        rm Miniconda3-latest-Linux-x86_64.sh
+
+        . /usr/bin/miniconda3/etc/profile.d/conda.sh
+        export PATH="/usr/bin/miniconda3/bin:$PATH"
+
+        #Conda configuration of channels from .condarc file
+        conda config --file /.condarc --add channels defaults
+        conda config --file /.condarc --add channels conda-forge
+        conda update conda
+        #List installed environments
+        conda list
+        conda install mamba -n base -c conda-forge
+
+    %labels
+        Author [email protected]
+        Version 1.2.0
+        Pipeline Iliad-Genomic-Data-Pipeline
+        SoftwareToolsVersion 1.16
 
 
 Docker 'definition' file
 ========================
 
 .. code-block:: none 
 
-    Testing
+    FROM ubuntu:20.04
+
+    MAINTAINER	Noah Herrick	<[email protected]>
+    ARG BCFTOOLS_VERSION=1.16
+    ARG SAMTOOLS_VERSION=1.16
+    ARG GTC2VCF_VERSION=1.14
+    ENV PATH /usr/bin:/usr/bin/bcftools-1.16/bin/:/usr/bin/samtools-1.16/bin/:/usr/bin/miniconda3/bin:${PATH}
+
+    RUN apt-get -y update \
+    && apt -y update \
+    && apt install software-properties-common -y \
+    && apt-get install -y \
+    wget \
+    bwa \
+    curl \
+    git \
+    tar \
+    build-essential \
+    zlib1g-dev \
+    libbz2-dev \
+    liblzma-dev \
+    libncurses5-dev \
+    unzip \
+    screen \
+    less \
+    nano && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
+
+    RUN export PATH && \
+    export BCFTOOLS_PLUGINS=/usr/bin/bcftools-${BCFTOOLS_VERSION}/plugins/ 
+
+    RUN wget -P /usr/bin/ https://github.com/samtools/bcftools/releases/download/${BCFTOOLS_VERSION}/bcftools-${BCFTOOLS_VERSION}.tar.bz2 && \
+    cd /usr/bin && \
+    tar -xf bcftools-${BCFTOOLS_VERSION}.tar.bz2
+    WORKDIR /usr/bin/bcftools-${BCFTOOLS_VERSION}
+    RUN ./configure --prefix=/usr/bin/bcftools-${BCFTOOLS_VERSION} && make && make install && \
+    export PATH="/usr/bin/bcftools-${BCFTOOLS_VERSION}/bin:$PATH" && \
+    rm /usr/bin/bcftools-${BCFTOOLS_VERSION}.tar.bz2
+
+    RUN wget -P /usr/bin/ https://sourceforge.net/projects/samtools/files/samtools/${SAMTOOLS_VERSION}/samtools-${SAMTOOLS_VERSION}.tar.bz2 && \
+    cd /usr/bin/ && \
+    tar xvfj /usr/bin/samtools-${SAMTOOLS_VERSION}.tar.bz2 && \
+    cd /usr/bin/samtools-${SAMTOOLS_VERSION}/ && \
+    ./configure --prefix=/usr/bin/samtools-${SAMTOOLS_VERSION} && make && make install && \
+    export PATH="/usr/bin/samtools-${SAMTOOLS_VERSION}/bin:$PATH" && \
+    rm /usr/bin/samtools-${SAMTOOLS_VERSION}.tar.bz2
+
+    RUN wget -P /usr/bin/bcftools-${BCFTOOLS_VERSION}/plugins/ https://software.broadinstitute.org/software/gtc2vcf/gtc2vcf_${GTC2VCF_VERSION}-20220112.zip && \
+    cd /usr/bin/bcftools-${BCFTOOLS_VERSION}/plugins/ && \
+    unzip gtc2vcf_${GTC2VCF_VERSION}-20220112.zip
+
+    # Install miniconda
+    ENV CONDA_DIR /opt/conda
+    RUN wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda.sh && \
+    /bin/bash ~/miniconda.sh -b -p /opt/conda
+
+    # Put conda in path so we can use conda activate
+    ENV PATH=$CONDA_DIR/bin:$PATH
+
+    RUN mkdir -p /usr/projects/ && cd /usr/projects/
+
+    SHELL ["/bin/bash", "-c"]
+
+    RUN conda init bash
+
+    RUN source ~/.bashrc