<commit_before>Bootstrap: docker
From: ubuntu:xenial

%help
    This is a container for installing expansionhunter version 3.1.2

%labels
    Maintainer Clinical-Genomics/MIP
    Version 0.1

%environment
    SHELL=/bin/bash
    PATH=/opt/conda/bin:${PATH}
    LC_ALL=C.UTF-8

%runscript
    export PATH=/opt/conda/bin:${PATH}
    "$@"

%post
    ## Set up sytem programs and libraries
    apt-get update --fix-missing && \
    apt-get install -y \
        build-essential \
        coreutils \
        dialog \
        git \
        language-pack-en-base \
        libbz2-dev \
        libcurl4-openssl-dev \
        liblzma-dev \
        libncurses5-dev \
        libncursesw5-dev \
        libreadline-dev \
        libssl-dev \
        tar \
        unzip \
        wget \
        zlib1g-dev && \
    apt-get clean
    update-locale LC_ALL=en_US.UTF-8 LANG=en_US.UTF-8

    ## Set up conda
    wget https://repo.anaconda.com/miniconda/Miniconda3-4.7.10-Linux-x86_64.sh && \
    /bin/bash ./Miniconda3-4.7.10-Linux-x86_64.sh -b -p /opt/conda/ && \
    rm Miniconda3-4.7.10-Linux-x86_64.sh && \
    ln -s /opt/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh

    export PATH=/opt/conda/bin:${PATH}
    conda config --add channels defaults
    conda config --add channels conda-forge
    conda config --add channels bioconda

    wget --no-verbose https://github.com/Illumina/ExpansionHunter/releases/download/v3.1.2/ExpansionHunter-v3.1.2-linux_x86_64.tar.gz -O ExpansionHunter-v3.1.2-linux_x86_64.tar.gz

    tar --extract --file=ExpansionHunter-v3.1.2-linux_x86_64.tar.gz --directory=/opt/conda/share/

    chmod -R 755 /opt
    chmod a+x /opt/conda/share/ExpansionHunter-v3.1.2-linux_x86_64/bin/ExpansionHunter
    ln --symbolic --force /opt/conda/share/ExpansionHunter-v3.1.2-linux_x86_64/bin/ExpansionHunter /opt/conda/bin/

    rm --recursive ExpansionHunter-v3.1.2-linux_x86_64.tar.gz<commit_msg>feat(exp_sif): Now installing in opt<commit_after>Bootstrap: docker
From: ubuntu:xenial

%help
    This is a container for installing expansionhunter version 3.1.2

%labels
    Maintainer Clinical-Genomics/MIP
    Version 0.1

%environment
    SHELL=/bin/bash
    PATH=/opt/conda/bin:${PATH}
    LC_ALL=C.UTF-8

%runscript
    export PATH=/opt/conda/bin:${PATH}
    "$@"

%post
    ## Set up sytem programs and libraries
    apt-get update --fix-missing && \
    apt-get install -y \
        build-essential \
        coreutils \
        dialog \
        git \
        language-pack-en-base \
        libbz2-dev \
        libcurl4-openssl-dev \
        liblzma-dev \
        libncurses5-dev \
        libncursesw5-dev \
        libreadline-dev \
        libssl-dev \
        tar \
        unzip \
        wget \
        zlib1g-dev && \
    apt-get clean
    update-locale LC_ALL=en_US.UTF-8 LANG=en_US.UTF-8

    ## Set up conda
    wget https://repo.anaconda.com/miniconda/Miniconda3-4.7.10-Linux-x86_64.sh && \
    /bin/bash ./Miniconda3-4.7.10-Linux-x86_64.sh -b -p /opt/conda/ && \
    rm Miniconda3-4.7.10-Linux-x86_64.sh && \
    ln -s /opt/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh

    export PATH=/opt/conda/bin:${PATH}
    conda config --add channels defaults
    conda config --add channels conda-forge
    conda config --add channels bioconda

    wget --no-verbose https://github.com/Illumina/ExpansionHunter/releases/download/v3.1.2/ExpansionHunter-v3.1.2-linux_x86_64.tar.gz -O /opt/conda/share/ExpansionHunter-v3.1.2-linux_x86_64.tar.gz

    tar --extract --file=/opt/conda/share/ExpansionHunter-v3.1.2-linux_x86_64.tar.gz --directory=/opt/conda/share/

    ln --symbolic --force /opt/conda/share/ExpansionHunter-v3.1.2-linux_x86_64/bin/ExpansionHunter /opt/conda/bin/

    rm --recursive /opt/conda/share/ExpansionHunter-v3.1.2-linux_x86_64.tar.gz
{'fraction_non_alphanumeric': 0.1331571994715984, 'fraction_numerical': 0.043857331571994715, 'mean_word_length': 2.2139219015280136, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 4, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 2, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '6950373', 'n_tokens_mistral': 1594, 'n_tokens_neox': 1455, 'n_words': 230}