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Singularity.guppy4.5.4gpu-conda-api
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Singularity.guppy4.5.4gpu-conda-api
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Bootstrap: docker
From: tensorflow/tensorflow:2.4.1-gpu
# Using an image based on Ubuntu 18.04
%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
export DEBIAN_FRONTEND=noninteractive
apt update
apt install -y git wget rsync zlib1g-dev dpkg python3-pip tzdata
#### Miniconda
# install miniconda
if [ ! -d /opt/conda ]; then
wget https://repo.anaconda.com/miniconda/Miniconda3-4.7.12.1-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:$PATH"
# update conda
conda update -n base -c defaults conda
# activate conda
#eval "$(/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 GPU
GUPPY_VERSION=4.5.4
# apt-get update && \
# apt-get install --yes \
# apt-transport-https \
# libcurl4-openssl-dev \
# libssl-dev \
# libhdf5-cpp-11 \
# libzmq5 \
# libboost-atomic1.58.0 \
# libboost-chrono1.58.0 \
# libboost-date-time1.58.0 \
# libboost-filesystem1.58.0 \
# libboost-program-options1.58.0 \
# libboost-regex1.58.0 \
# libboost-system1.58.0 \
# libboost-log1.58.0 \
# libboost-iostreams1.58.0 \
# wget && \
# cd /tmp &&\
# wget -q https://mirror.oxfordnanoportal.com/software/analysis/ont_guppy_${GUPPY_VERSION}-1~bionic_amd64.deb && \
# dpkg -i --ignore-depends=nvidia-384,libcuda1-384 /tmp/ont_guppy_${GUPPY_VERSION}-1~bionic_amd64.deb && \
# rm *.deb && \
apt-get update
apt-get install wget lsb-release
export PLATFORM=$(lsb_release -cs)
wget -O- https://mirror.oxfordnanoportal.com/apt/ont-repo.pub | apt-key add -
echo "deb http://mirror.oxfordnanoportal.com/apt ${PLATFORM}-stable non-free" | tee /etc/apt/sources.list.d/nanoporetech.sources.list
apt-get update
apt-get -y install ont-guppy=${GUPPY_VERSION}-1~${PLATFORM} --no-install-recommends
apt-get autoremove --purge --yes && \
apt-get clean && \
rm -rf /var/lib/apt/lists/*
#### INSTALL ONT_FAST5_API
pip install ont-fast5-api==3.1.3
%environment
export PATH="/opt/conda/bin:$PATH"