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Singularity.guppy3.4gpu-conda-api
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Singularity.guppy3.4gpu-conda-api
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Bootstrap: docker
From: tensorflow/tensorflow:1.13.1-gpu-py3
#From: nvidia/cuda:10.2-cudnn7-devel-ubuntu16.04
# Using an image based on Ubuntu 16.04 (required for Guppy to install...)
%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 zlib1g-dev dpkg python3-pip tzdata
#### 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:$PATH"
# update conda
conda update -n base -c defaults conda
# activate conda
#eval "$(/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=3.4.3
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_${GUPPY_VERSION}-1~xenial_amd64.deb && \
dpkg -i --ignore-depends=nvidia-384,libcuda1-384 /tmp/ont_guppy_${GUPPY_VERSION}-1~xenial_amd64.deb && \
rm *.deb && \
apt-get autoremove --purge --yes && \
apt-get clean && \
rm -rf /var/lib/apt/lists/*
#### INSTALL ONT_FAST5_API
python3 -m pip install git+https://github.com/nanoporetech/ont_fast5_api
%environment
export PATH="/opt/conda/bin:$PATH"
%runscript
echo "Now inside Singularity container woah..."
exec /bin/bash