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Singularity.guppy3.6.0cpu-conda-api
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Singularity.guppy3.6.0cpu-conda-api
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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/Miniconda3-4.7.12.1-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:$PATH"
# activate conda
#eval "$(/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=3.6.0
apt update && \
apt-get install --yes apt-transport-https && \
cd /tmp && \
wget -q https://mirror.oxfordnanoportal.com/software/analysis/ont_guppy_cpu_${GUPPY_VERSION}-1~xenial_amd64.deb && \
apt-get install --yes libzmq5 libhdf5-cpp-11 \
libcurl4-openssl-dev libssl-dev libhdf5-10 \
libboost-regex1.58.0 libboost-log1.58.0 \
libboost-atomic1.58.0 libboost-chrono1.58.0 \
libboost-date-time1.58.0 libboost-filesystem1.58.0 \
libboost-program-options1.58.0 libboost-iostreams1.58.0 && \
dpkg -i *.deb && \
rm *.deb && \
apt-get autoremove --purge --yes && \
apt-get clean && \
rm -rf /var/lib/apt/lists/*
#### GUPPY CPU ONT_FAST5_API
# pip3 install git+https://github.com/nanoporetech/ont_fast5_api
pip install ont-fast5-api==3.1.3
%environment
export PATH="/opt/conda/bin:$PATH"