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Bootstrap: library
From: ubuntu:18.04
%environment
export PATH="/usr/local/bin:$PATH"
%help
This container launches megalodon software used for the identification of modified nucleotides from nanopore sequencing data.
======================================================================================
usage (help) : singularity run megalodon.sif
building container : singularity build tombo.sif tombo.def
======================================================================================
%post
# ================================
# PREPARE the system
# ================================
export DEBIAN_FRONTEND=noninteractive
apt-get update
apt-get install -y software-properties-common
apt-add-repository universe
apt-get update
export LC_ALL=C.UTF-8
export LANG=C.UTF-8
echo 'export LC_ALL=C.UTF-8' >> "$SINGULARITY_ENVIRONMENT"
echo 'export LANG=C.UTF-8' >> "$SINGULARITY_ENVIRONMENT"
apt-get install -y \
wget \
build-essential
libboostVERSION="1.62.0"
apt-get install -y \
libidn11 \
libidn11-dev \
libgssapi-krb5-2 \
libboost-atomic${libboostVERSION} \
libboost-chrono${libboostVERSION} \
libboost-date-time${libboostVERSION} \
libboost-filesystem${libboostVERSION} \
libboost-program-options${libboostVERSION} \
libboost-regex${libboostVERSION} \
libboost-system${libboostVERSION} \
libboost-log${libboostVERSION}
# ================================
# INSTALL python3.8
# ================================
apt-get -y install software-properties-common
add-apt-repository ppa:deadsnakes/ppa
apt-get -y install python3.8-distutils
apt-get -y install python3.8
ln -s /usr/bin/python3.8 /usr/bin/python
# ================================
# INSTALL guppy-cpu
# ================================
VERSION="6.0.1"
URL="https://mirror.oxfordnanoportal.com/software/analysis/ont-guppy-cpu_6.0.1_linux64.tar.gz"
wget "$URL" -O - | tar xzf -
cd ont-guppy-cpu || exit 1
for binary in bin/guppy_*
do
ln -s "$(realpath "$binary")" "/usr/local/bin/$(basename "$binary")"
done
# ================================
# INSTALL conda
# ================================
wget -c https://repo.anaconda.com/archive/Anaconda3-2020.02-Linux-x86_64.sh
/bin/bash Anaconda3-2020.02-Linux-x86_64.sh -bfp /usr/local
#Conda configuration of channels from .condarc file
conda config --file /.condarc --add channels defaults
conda config --file /.condarc --add channels conda-forge
conda update conda
##Install Guppy
VERSION="6.0.1"
URL="https://mirror.oxfordnanoportal.com/software/analysis/ont-guppy-cpu_6.0.1_linux64.tar.gz"
wget "$URL" -O - | tar xzf -
cd ont-guppy-cpu || exit 1
for binary in bin/guppy_*
do
ln -s -f "$(realpath "$binary")" "/usr/local/bin/$(basename "$binary")"
done
pip install ont-pyguppy-client-lib==6.0.1
# ================================
# INSTALL MEGALODON
# ================================
pip install megalodon