ont-bonito Singularity definition

gistfile1.txt

BootStrap: docker
From: nvidia/cuda:11.2.0-cudnn8-devel-ubuntu20.04

%post

    export LC_ALL=C.UTF-8
    export LANG=C.UTF-8
    echo 'export LC_ALL=C.UTF-8' >>  $SINGULARITY_ROOTFS/$SINGULARITY_ENVIRONMENT
    echo 'export LANG=C.UTF-8' >>  $SINGULARITY_ROOTFS/$SINGULARITY_ENVIRONMENT

    export MAKEFLAGS="-j 8 "

    ### Avoid useless deb packages
    echo 'APT::Install-Recommends "0";' > /etc/apt/apt.conf.d/10norecommends
    echo 'APT::Install-Suggests "0";' >>  /etc/apt/apt.conf.d/10norecommends

    echo 'debconf debconf/frontend select Noninteractive' | debconf-set-selections

    apt update
    apt install -y nano wget build-essential git autoconf automake build-essential \
                   bzip2 ca-certificates libglib2.0-dev libxext6 libsm6 libxrender1 libhdf5-dev

    # install miniconda
    CONDA_DIR=/opt/conda
    wget  https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O /miniconda.sh
    sh /miniconda.sh -b -p $CONDA_DIR
    rm /miniconda.sh
    # make non-activate conda commands available
    export PATH=$CONDA_DIR/bin:$PATH

    conda update -n base -c defaults conda

    APP=ont-bonito
    VER=0.3.8
    ENV_NAME=${APP}_${VER}_singularity
    ENV_BIN_DIR=$CONDA_DIR/envs/$ENV_NAME/bin

    conda create --no-default-packages --name $ENV_NAME
    conda install --name $ENV_NAME numpy ninja pyyaml mkl mkl-include setuptools cmake cffi typing_extensions future six requests dataclasses fastrlock
    conda install --name $ENV_NAME -c pytorch magma-cuda112
    conda install --name $ENV_NAME -c conda-forge cudatoolkit=11.2.2
    conda install --name $ENV_NAME -c intel cython

    export PATH=$ENV_BIN_DIR:$PATH

    # build cupy from src, otherwise install cupy-cuda112
    cd /
    git clone --recursive https://github.com/cupy/cupy.git
    cd cupy
    $ENV_BIN_DIR/python setup.py install

    # build seqdist with new cupy
    cd /
    git clone https://github.com/davidcpage/seqdist.git
    cd seqdist
    perl -npi -e 's/cupy-cuda102/cupy/' settings.ini
    $ENV_BIN_DIR/python setup.py install
    cd /

    # build pytorch for CUDA 11.2, takes about 80 minutes  :-(
    git clone --recursive https://github.com/pytorch/pytorch
    cd pytorch
    export CMAKE_PREFIX_PATH=${CONDA_PREFIX:-"$(dirname $(which conda))/../"}
    $ENV_BIN_DIR/python setup.py install

    # build ont-bonito with our new versions for CUDA 11.2
    cd /
    git clone -b v${VER} https://github.com/nanoporetech/bonito.git
    cd bonito
    # remove these requirements as we already have them installed with good versions
    perl -npi -e 's/torch==1.8.0//' requirements.txt
    perl -npi -e 's/seqdist==0.0.3//' requirements.txt
    perl -npi -e 's/numpy<=1.18.5//' requirements.txt
    $ENV_BIN_DIR/pip3 install -r requirements.txt
    $ENV_BIN_DIR/python setup.py install

    # cleanup src dirs
    cd /
    rm -rf /cupy
    rm -rf /seqdist
    rm -rf /pytorch

    # Finally have a cleanup of conda to save space in the containerq
    conda clean -afy  \
    && find /opt/conda/ -follow -type f -name '*.a' -delete \
    && find /opt/conda/ -follow -type f -name '*.pyc' -delete \
    && find /opt/conda/ -follow -type f -name '*.js.map' -delete

    # And set the env to auto-start when you exec a command
    mkdir -p $SINGULARITY_ROOTFS/.singularity.d/env
    echo "source /opt/conda/etc/profile.d/conda.sh" >> $SINGULARITY_ROOTFS/$SINGULARITY_ENVIRONMENT
    echo "conda activate $ENV_NAME" >> $SINGULARITY_ROOTFS/$SINGULARITY_ENVIRONMENT

%environment

%runscript
    exec "$@"