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| Original file line number | Diff line number | Diff line change |
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| @@ -1,73 +1,80 @@ | ||
| BootStrap: docker | ||
| From: ubuntu:latest | ||
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| %labels | ||
| AUTHOR Nicolas Servant | ||
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| %pre | ||
| apt-get install -y debootstrap | ||
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| %files | ||
| environment.yml /opt/environment.yml | ||
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| %post | ||
| apt-get update | ||
| apt-get install -y wget | ||
| apt-get install -y gzip | ||
| apt-get install -y bzip2 | ||
| apt-get install -y curl | ||
| apt-get install -y unzip | ||
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| ## g++ | ||
| apt-get install -y build-essential | ||
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| # install anaconda | ||
| if [ ! -d /usr/local/anaconda ]; then | ||
| wget https://repo.continuum.io/miniconda/Miniconda3-4.5.4-Linux-x86_64.sh \ | ||
| -O ~/anaconda.sh && \ | ||
| bash ~/anaconda.sh -b -p /usr/local/anaconda && \ | ||
| rm ~/anaconda.sh | ||
| fi | ||
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| # set anaconda path | ||
| export PATH=$PATH:/usr/local/anaconda/bin | ||
| conda update conda | ||
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| conda config --add channels r | ||
| conda config --add channels defaults | ||
| conda config --add channels conda-forge | ||
| conda config --add channels bioconda | ||
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| # Let us save some space | ||
| conda clean --packages -y | ||
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| # external tools | ||
| echo "Installing conda environment ... " | ||
| conda env create -f /opt/environment.yml | ||
| echo "source activate HiC-Pro_v3.1.0" > ~/.bashrc | ||
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| # Install HiC-pro | ||
| echo "Installing latest HiC-Pro release ..." | ||
| VERSION=$(curl -s https://github.com/nservant/HiC-Pro/releases/latest | egrep -o 'v3.[0-9]*.[0-9]*') | ||
| echo "v"$VERSION".zip" | wget --base=http://github.com/nservant/HiC-Pro/archive/ -i - -O hicpro_latest.zip && unzip hicpro_latest.zip | ||
| #VERSION="devel_py3" | ||
| #echo $VERSION".zip" | wget --base=http://github.com/nservant/HiC-Pro/archive/ -i - -O hicpro_latest.zip && unzip hicpro_latest.zip | ||
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| cd $(echo HiC-Pro-$VERSION) | ||
| make configure | ||
| make install | ||
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| # Let us save some space | ||
| conda clean --packages -y | ||
| conda clean --all -y | ||
| rm -rf /usr/local/anaconda/pkgs | ||
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| %test | ||
| INSTALLED_HICPRO_VERSION=$(find /usr/local/bin -name HiC-Pro | xargs dirname) | ||
| $INSTALLED_HICPRO_VERSION/HiC-Pro -h | ||
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| %environment | ||
| export PATH=$PATH:/usr/local/anaconda/bin | ||
| INSTALLED_VERSION=$(find /usr/local/bin -name HiC-Pro | xargs dirname) | ||
| export PATH=$PATH:$INSTALLED_VERSION | ||
| export LANG=C | ||
| BootStrap: docker | ||
| From: ubuntu:latest | ||
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| %labels | ||
| AUTHOR Nicolas Servant | ||
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| %files | ||
| environment.yml /opt/environment.yml | ||
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| %environment | ||
| export LANG=en_US.utf-8 | ||
| export INSTALLED_VERSION=$(find /usr/local/bin -name HiC-Pro | xargs dirname) | ||
| export PATH=$PATH:${INSTALLED_VERSION}:${INSTALLED_VERSION}/utils/ | ||
| export PATH=/usr/local/conda/bin:$PATH | ||
| source /opt/etc/bashrc | ||
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| %post | ||
| apt-get update && \ | ||
| apt-get install -y \ | ||
| wget \ | ||
| debootstrap \ | ||
| gzip \ | ||
| bzip2 \ | ||
| curl \ | ||
| unzip \ | ||
| g++ \ | ||
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| # use bash as /bin/sh instead of dash (otherwise source /opt/etc/bashrc will not work) | ||
| echo "dash dash/sh boolean false" | debconf-set-selections | ||
| DEBIAN_FRONTEND=noninteractive dpkg-reconfigure dash | ||
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| # install miniconda | ||
| if [ ! -d /usr/local/miniconda ]; then | ||
| wget https://repo.continuum.io/miniconda/Miniconda3-py39_4.10.3-Linux-x86_64.sh -O miniconda.sh && \ | ||
| sh miniconda.sh -b -p /usr/local/conda && \ | ||
| rm miniconda.sh && \ | ||
| ln -s /usr/local/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh && \ | ||
| find /usr/local/conda/ -follow -type f -name '*.a' -delete && \ | ||
| find /usr/local/conda/ -follow -type f -name '*.js.map' -delete && \ | ||
| /usr/local/conda/bin/conda clean -afy | ||
| fi | ||
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| # set miniconda path | ||
| export PATH=/usr/local/conda/bin:$PATH | ||
| conda update conda | ||
| conda clean --packages -y | ||
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| #bashrc | ||
| echo "#! /bin/bash\n\n" > ~/.bashrc | ||
| conda init bash | ||
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| # external tools | ||
| echo "Installing conda environment ... " | ||
| conda env create -f /opt/environment.yml -n hicpro | ||
| echo "conda activate hicpro" >> ~/.bashrc | ||
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| # Install HiC-pro | ||
| export PATH=/usr/local/conda/envs/hicpro/bin:$PATH | ||
| echo "Installing latest HiC-Pro release ..." | ||
| #VERSION=$(curl -s https://github.com/nservant/HiC-Pro/releases/latest | egrep -o 'v3.[0-9]*.[0-9]*') | ||
| VERSION="3.1.0" | ||
| echo "v"$VERSION".zip" | wget --base=http://github.com/nservant/HiC-Pro/archive/ -i - -O hicpro_latest.zip && unzip hicpro_latest.zip | ||
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| cd $(echo HiC-Pro-$VERSION) | ||
| make configure | ||
| make install | ||
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| # Let us save some space | ||
| conda clean --packages -y | ||
| conda clean --all -y | ||
| rm -rf /usr/local/miniconda/pkgs | ||
| apt-get clean | ||
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| mkdir /opt/etc/ | ||
| cp ~/.bashrc /opt/etc/bashrc | ||
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| %test | ||
| INSTALLED_HICPRO_VERSION=$(find /usr/local/bin -name HiC-Pro | xargs dirname) | ||
| ${INSTALLED_HICPRO_VERSION}/HiC-Pro -h | ||
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