Singularity.cpu-guppy3.4-conda-api

Bootstrap: docker
#From: tensorflow/tensorflow:1.13.1-py3
From: nvidia/cuda:10.2-cudnn7-devel-ubuntu16.04

# Using an image based on Ubuntu 16.04 (required for Guppy to install...)

%labels
MAINTAINER vibaotram

%help
  A container to hold the nanopore barcode demultiplexer guppy cpu version and Miniconda3.

%post
    echo 'export LC_ALL=C.UTF-8' >> /environment
    echo 'export LANG=C.UTF-8' >> /environment
    export LC_ALL=C.UTF-8
    export LANG=C.UTF-8
    apt update
    apt install -y git wget rsync tzdata dpkg python3-pip zlib1g-dev

#### Miniconda
    # install miniconda
    if [ ! -d /opt/conda ]; then
         wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh \
            -O ~/miniconda.sh && \
         bash ~/miniconda.sh -b -p /opt/conda && \
         rm ~/miniconda.sh && \
         /opt/conda/bin/conda clean -tipsy && \
         ln -s /opt/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh && \
         echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc && \
         echo "conda activate base" >> ~/.bashrc
    fi
    # set miniconda path
    export PATH="/opt/conda/bin:$PATH"

    # activate conda
    #eval "$(/opt/conda/bin/conda shell.bash hook)"
    # configuring channels
    conda config --add channels defaults
    conda config --add channels bioconda
    conda config --add channels conda-forge


#### GUPPY CPU
    GUPPY_VERSION=3.4.3
    apt update && \
    apt-get install --yes apt-transport-https && \
    cd /tmp && \
    wget -q https://mirror.oxfordnanoportal.com/software/analysis/ont_guppy_cpu_${GUPPY_VERSION}-1~xenial_amd64.deb && \
    apt-get install --yes libzmq5 libhdf5-cpp-11 \
                          libcurl4-openssl-dev libssl-dev libhdf5-10 \
                          libboost-regex1.58.0 libboost-log1.58.0 \
                          libboost-atomic1.58.0 libboost-chrono1.58.0 \
                          libboost-date-time1.58.0 libboost-filesystem1.58.0 \
                          libboost-program-options1.58.0 libboost-iostreams1.58.0 && \
    dpkg -i *.deb && \
    rm *.deb && \
    apt-get autoremove --purge --yes && \
    apt-get clean && \
    rm -rf /var/lib/apt/lists/*




    #================================
    # INSTALL ONT_FAST5_API
    #================================
    pip3 install git+https://github.com/nanoporetech/ont_fast5_api


%environment
  export PATH="/opt/conda/bin:$PATH"