FSL Alpine Docker Install

FSL_Alpine_Dockerfile

FROM alpine:latest

ENV LANG=C.UTF-8
ENV FSLDIR="/opt/miniconda/envs/FSL/share/fsl"
ENV PATH="$FSLDIR/bin:$PATH"
ENV TERM=xterm
ENV CONDA_OVERRIDE_GLIBC=2.34
ENV CONDA_ALWAYS_YES=true
ENV CONDA_AUTO_UPDATE_CONDA=false
# ENV MAMBA_ROOT_PREFIX=/opt/miniconda

RUN apk update && \
    apk add --no-cache \
        ca-certificates \
        openssl \
        curl && \
    mkdir -p /usr/local/share/ca-certificates

# Add both G2 root and L1K intermediate certificates
RUN printf '%s\n' \
    '-----BEGIN CERTIFICATE-----' \
    'MIIEPjCCAyagAwIBAgIESlOMKDANBgkqhkiG9w0BAQsFADCBvjELMAkGA1UEBhMC' \
    'VVMxFjAUBgNVBAoTDUVudHJ1c3QsIEluYy4xKDAmBgNVBAsTH1NlZSB3d3cuZW50' \
    'cnVzdC5uZXQvbGVnYWwtdGVybXMxOTA3BgNVBAsTMChjKSAyMDA5IEVudHJ1c3Qs' \
    'IEluYy4gLSBmb3IgYXV0aG9yaXplZCB1c2Ugb25seTEyMDAGA1UEAxMpRW50cnVz' \
    'dCBSb290IENlcnRpZmljYXRpb24gQXV0aG9yaXR5IC0gRzIwHhcNMDkwNzA3MTcy' \
    'NTU0WhcNMzAxMjA3MTc1NTU0WjCBvjELMAkGA1UEBhMCVVMxFjAUBgNVBAoTDUVu' \
    'dHJ1c3QsIEluYy4xKDAmBgNVBAsTH1NlZSB3d3cuZW50cnVzdC5uZXQvbGVnYWwt' \
    'dGVybXMxOTA3BgNVBAsTMChjKSAyMDA5IEVudHJ1c3QsIEluYy4gLSBmb3IgYXV0' \
    'aG9yaXplZCB1c2Ugb25seTEyMDAGA1UEAxMpRW50cnVzdCBSb290IENlcnRpZmlj' \
    'YXRpb24gQXV0aG9yaXR5IC0gRzIwggEiMA0GCSqGSIb3DQEBAQUAA4IBDwAwggEK' \
    'AoIBAQC6hLZy254Ma+KZ6TABp3bqMriVQRrJ2mFOWHLP/vaCeb9zYQYKpSfYs1/T' \
    'RU4cctZOMvJyig/3gxnQaoCAAEUesMfnmr8SVycco2gvCoe9amsOXmXzHHfV1IWN' \
    'cCG0szLni6LVhjkCsbjSR87kyUnEO6fe+1R9V77w6G7CebI6C1XiUJgWMhNcL3hW' \
    'wcKUs/Ja5CeanyTXxuzQmyWC48zCxEXFjJd6BmsqEZ+pCm5IO2/b1BEZQvePB7/1' \
    'U1+cPvQXLOZprE4yTGJ36rfo5bs0vBmLrpxR57d+tVOxMyLlbc9wPBr64ptntoP0' \
    'jaWvYkxN4FisZDQSA/i2jZRjJKRxAgMBAAGjQjBAMA4GA1UdDwEB/wQEAwIBBjAP' \
    'BgNVHRMBAf8EBTADAQH/MB0GA1UdDgQWBBRqciZ60B7vfec7aVHUbI2fkBJmqzAN' \
    'BgkqhkiG9w0BAQsFAAOCAQEAeZ8dlsa2eT8ijYfThwMEYGprmi5ZiXMRrEPR9RP/' \
    'jTkrwPK9T3CMqS/qF8QLVJ7UG5aYMzyorWKiAHarWWluBh1+xLlEjZivEtRh2woZ' \
    'Rkfz6/djwUAFQKXSt/S1mja/qYh2iARVBCuch38aNzx+LaUa2NSJXsq9rD1s2G2v' \
    '1fN2D807iDginWyTmsQ9v4IbZT+mD12q/OWyFcq1rca8PdCE6OoGcrBNOTJ4vz4R' \
    'nAuknZoh8/CbCzB428Hch0P+vGOaysXCHMnHjf87ElgI5rY97HosTvuDls4MPGmH' \
    'VHOkc8KT/1EQrBVUAdj8BbGJoX90g5pJ19xOe4pIb4tF9g==' \
    '-----END CERTIFICATE-----' > /usr/local/share/ca-certificates/entrust-g2.crt && \
    printf '%s\n' \
    '-----BEGIN CERTIFICATE-----' \
    'MIIFDjCCA/agAwIBAgIMDulMwwAAAABR03eFMA0GCSqGSIb3DQEBCwUAMIG+MQsw' \
    'CQYDVQQGEwJVUzEWMBQGA1UEChMNRW50cnVzdCwgSW5jLjEoMCYGA1UECxMfU2Vl' \
    'IHd3dy5lbnRydXN0Lm5ldC9sZWdhbC10ZXJtczE5MDcGA1UECxMwKGMpIDIwMDkg' \
    'RW50cnVzdCwgSW5jLiAtIGZvciBhdXRob3JpemVkIHVzZSBvbmx5MTIwMAYDVQQD' \
    'EylFbnRydXN0IFJvb3QgQ2VydGlmaWNhdGlvbiBBdXRob3JpdHkgLSBHMjAeFw0x' \
    'NTEwMDUxOTEzNTZaFw0zMDEyMDUxOTQzNTZaMIG6MQswCQYDVQQGEwJVUzEWMBQG' \
    'A1UEChMNRW50cnVzdCwgSW5jLjEoMCYGA1UECxMfU2VlIHd3dy5lbnRydXN0Lm5l' \
    'dC9sZWdhbC10ZXJtczE5MDcGA1UECxMwKGMpIDIwMTIgRW50cnVzdCwgSW5jLiAt' \
    'IGZvciBhdXRob3JpemVkIHVzZSBvbmx5MS4wLAYDVQQDEyVFbnRydXN0IENlcnRp' \
    'ZmljYXRpb24gQXV0aG9yaXR5IC0gTDFLMIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8A' \
    'MIIBCgKCAQEA2j+W0E25L0Tn2zlem1DuXKVh2kFnUwmqAJqOV38pa9vH4SEkqjrQ' \
    'jUcj0u1yFvCRIdJdt7hLqIOPt5EyaM/OJZMssn2XyP7BtBe6CZ4DkJN7fEmDImiK' \
    'm95HwzGYei59QAvS7z7Tsoyqj0ip/wDoKVgG97aTWpRzJiatWA7lQrjV6nN5ZGhT' \
    'JbiEz5R6rgZFDKNrTdDGvuoYpDbwkrK6HIiPOlJ/915tgxyd8B/lw9bdpXiSPbBt' \
    'LOrJz5RBGXFEaLpHPATpXbo+8DX3Fbae8i4VHj9HyMg4p3NFXU2wO7GOFyk36t0F' \
    'ASK7lDYqjVs1/lMZLwhGwSqzGmIdTivZGwIDAQABo4IBDDCCAQgwDgYDVR0PAQH/' \
    'BAQDAgEGMBIGA1UdEwEB/wQIMAYBAf8CAQAwMwYIKwYBBQUHAQEEJzAlMCMGCCsG' \
    'AQUFBzABhhdodHRwOi8vb2NzcC5lbnRydXN0Lm5ldDAwBgNVHR8EKTAnMCWgI6Ah' \
    'hh9odHRwOi8vY3JsLmVudHJ1c3QubmV0L2cyY2EuY3JsMDsGA1UdIAQ0MDIwMAYE' \
    'VR0gADAoMCYGCCsGAQUFBwIBFhpodHRwOi8vd3d3LmVudHJ1c3QubmV0L3JwYTAd' \
    'BgNVHQ4EFgQUgqJwdN28Uz/Pe9T3zX+nYMYKTL8wHwYDVR0jBBgwFoAUanImetAe' \
    '733nO2lR1GyNn5ASZqswDQYJKoZIhvcNAQELBQADggEBADnVjpiDYcgsY9NwHRkw' \
    'y/YJrMxp1cncN0HyMg/vdMNY9ngnCTQIlZIv19+4o/0OgemknNM/TWgrFTEKFcxS' \
    'BJPok1DD2bHi4Wi3Ogl08TRYCj93mEC45mj/XeTIRsXsgdfJghhcg85x2Ly/rJkC' \
    'k9uUmITSnKa1/ly78EqvIazCP0kkZ9Yujs+szGQVGHLlbHfTUqi53Y2sAEo1GdRv' \
    'c6N172tkw+CNgxKhiucOhk3YtCAbvmqljEtoZuMrx1gL+1YQ1JH7HdMxWBCMRON1' \
    'exCdtTix9qrKgWRs6PLigVWXUX/hwidQosk8WwBD9lu51aX8/wdQQGcHsFXwt35u' \
    'Lcw=' \
    '-----END CERTIFICATE-----' > /usr/local/share/ca-certificates/entrust-l1k.crt && \
    update-ca-certificates

# Set certificate environment variables
ENV SSL_CERT_DIR=/etc/ssl/certs
ENV SSL_CERT_FILE=/etc/ssl/certs/ca-certificates.crt
ENV REQUESTS_CA_BUNDLE=/etc/ssl/certs/ca-certificates.crt

# Install glibc 2.34
RUN ALPINE_GLIBC_BASE_URL="https://github.com/sgerrand/alpine-pkg-glibc/releases/download" && \
    ALPINE_GLIBC_PACKAGE_VERSION="2.34-r0" && \
    ALPINE_GLIBC_BASE_PACKAGE_FILENAME="glibc-$ALPINE_GLIBC_PACKAGE_VERSION.apk" && \
    ALPINE_GLIBC_BIN_PACKAGE_FILENAME="glibc-bin-$ALPINE_GLIBC_PACKAGE_VERSION.apk" && \
    ALPINE_GLIBC_I18N_PACKAGE_FILENAME="glibc-i18n-$ALPINE_GLIBC_PACKAGE_VERSION.apk" && \
    apk add --no-cache --virtual=.build-dependencies wget ca-certificates && \
    echo \
        "-----BEGIN PUBLIC KEY-----\
        MIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEApZ2u1KJKUu/fW4A25y9m\
        y70AGEa/J3Wi5ibNVGNn1gT1r0VfgeWd0pUybS4UmcHdiNzxJPgoWQhV2SSW1JYu\
        tOqKZF5QSN6X937PTUpNBjUvLtTQ1ve1fp39uf/lEXPpFpOPL88LKnDBgbh7wkCp\
        m2KzLVGChf83MS0ShL6G9EQIAUxLm99VpgRjwqTQ/KfzGtpke1wqws4au0Ab4qPY\
        KXvMLSPLUp7cfulWvhmZSegr5AdhNw5KNizPqCJT8ZrGvgHypXyiFvvAH5YRtSsc\
        Zvo9GI2e2MaZyo9/lvb+LbLEJZKEQckqRj4P26gmASrZEPStwc+yqy1ShHLA0j6m\
        1QIDAQAB\
        -----END PUBLIC KEY-----" | sed 's/   */\n/g' > "/etc/apk/keys/sgerrand.rsa.pub" && \
    wget --no-verbose \
        "$ALPINE_GLIBC_BASE_URL/$ALPINE_GLIBC_PACKAGE_VERSION/$ALPINE_GLIBC_BASE_PACKAGE_FILENAME" \
        "$ALPINE_GLIBC_BASE_URL/$ALPINE_GLIBC_PACKAGE_VERSION/$ALPINE_GLIBC_BIN_PACKAGE_FILENAME" \
        "$ALPINE_GLIBC_BASE_URL/$ALPINE_GLIBC_PACKAGE_VERSION/$ALPINE_GLIBC_I18N_PACKAGE_FILENAME" && \
    mv /etc/nsswitch.conf /etc/nsswitch.conf.bak && \
    apk add --no-cache --force-overwrite \
        "$ALPINE_GLIBC_BASE_PACKAGE_FILENAME" \
        "$ALPINE_GLIBC_BIN_PACKAGE_FILENAME" \
        "$ALPINE_GLIBC_I18N_PACKAGE_FILENAME" && \
    mv /etc/nsswitch.conf.bak /etc/nsswitch.conf && \
    rm "/etc/apk/keys/sgerrand.rsa.pub" && \
    (/usr/glibc-compat/bin/localedef --force --inputfile POSIX --charmap UTF-8 "$LANG" || true) && \
    echo "export LANG=$LANG" > /etc/profile.d/locale.sh && \
    apk del glibc-i18n && \
    rm "/root/.wget-hsts" && \
    apk del .build-dependencies && \
    rm \
        "$ALPINE_GLIBC_BASE_PACKAGE_FILENAME" \
        "$ALPINE_GLIBC_BIN_PACKAGE_FILENAME" \
        "$ALPINE_GLIBC_I18N_PACKAGE_FILENAME"

# Install required packages
RUN apk add --no-cache \
    bash \
    libstdc++ \
    curl \
    sudo \
    python3 \
    py3-pip \
    python3-dev \
    bzip2 \
    tar \
    wget \
    file \
    bc \
    gcc \
    g++ \
    build-base \
    musl-dev \
    gzip \
    binutils \
    gtk+2.0 \
    firefox \
    pulseaudio \
    mesa-dev \
    mesa-dri-gallium \
    mesa-utils \
    mesa-gl \
    mesa-egl \
    mesa-gbm \
    libclc \
    libx11-dev

RUN adduser -D -s /bin/bash morphs && \
    echo "morphs ALL=(ALL) NOPASSWD:ALL" >> /etc/sudoers

WORKDIR /home/morphs

RUN curl -fsSL https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -o /tmp/Miniconda3.sh && \
    bash /tmp/Miniconda3.sh -b -p /opt/miniconda && \
    rm /tmp/Miniconda3.sh

ENV PATH="/opt/miniconda/bin:$PATH"

RUN conda install -n base -c conda-forge mamba

RUN wget https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fsl-6.0.7.9_linux-64.yml -O /tmp/fsl-6.0.7.9_linux-64.yml
RUN mamba create --yes --name FSL
RUN mamba install --yes --name FSL -f /tmp/fsl-6.0.7.9_linux-64.yml
RUN mamba clean --all --yes

USER morphs
WORKDIR /home/morphs

ENV PATH="/opt/miniconda/bin:$PATH"

RUN /opt/miniconda/bin/conda init bash && \
    echo "source /opt/miniconda/etc/profile.d/conda.sh" >> ~/.bashrc && \
    echo "conda activate FSL" >> ~/.bashrc && \
    bash -c "source ~/.bashrc && conda activate FSL && conda deactivate"

# Ensure Conda is available in all shells
ENV PATH="/opt/miniconda/bin:$PATH"

# Use bash as the entry point and force it to load the configuration
ENTRYPOINT [ "/bin/bash", "--rcfile", "/home/morphs/.bashrc", "-i" ]

https://fsl.fmrib.ox.ac.uk/fsl/docs/#/install/container

Entrust Root Certification Authority (EC1)
https://www.entrust.com/resources/tools/root-certificate-downloads

https://git.fmrib.ox.ac.uk/fsl

python-3.11.8

https://git.fmrib.ox.ac.uk/fsl/conda/fsl-base/-/blob/master/meta.yaml?ref_type=heads

conda-forge/miniforge#219
https://github.com/Docker-Hub-frolvlad/docker-alpine-glibc/blob/master/Dockerfile

https://neurostars.org/t/problems-installing-fsl/27620/57?page=3

https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/

Linking python-graphviz-0.20.3-pyh91182bf_2
Linking pyopengl-3.1.6-pyhd8ed1ab_2
/home/morphs/miniconda/envs/FSL/bin/.pyopengl-post-link.sh: line 11: 3249 Segmentation fault (core dumped) $PREFIX/bin/python -c "import OpenGL.GL"
Warning: Missing OpenGL driver, install with yum install mesa-libGL-devel or equivalent