diff --git a/containers/reprostim-timesync/Dockerfile b/containers/reprostim-timesync/Dockerfile deleted file mode 100644 index 3595c46..0000000 --- a/containers/reprostim-timesync/Dockerfile +++ /dev/null @@ -1,188 +0,0 @@ -# Generated by Neurodocker and Reproenv. - -FROM neurodebian:bookworm -ENV LANG="en_US.UTF-8" \ - LC_ALL="en_US.UTF-8" \ - ND_ENTRYPOINT="/neurodocker/startup.sh" -RUN export ND_ENTRYPOINT="/neurodocker/startup.sh" \ - && apt-get update -qq \ - && apt-get install -y -q --no-install-recommends \ - apt-utils \ - bzip2 \ - ca-certificates \ - curl \ - locales \ - unzip \ - && rm -rf /var/lib/apt/lists/* \ - && sed -i -e 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen \ - && dpkg-reconfigure --frontend=noninteractive locales \ - && update-locale LANG="en_US.UTF-8" \ - && chmod 777 /opt && chmod a+s /opt \ - && mkdir -p /neurodocker \ - && if [ ! -f "$ND_ENTRYPOINT" ]; then \ - echo '#!/usr/bin/env bash' >> "$ND_ENTRYPOINT" \ - && echo 'set -e' >> "$ND_ENTRYPOINT" \ - && echo 'export USER="${USER:=`whoami`}"' >> "$ND_ENTRYPOINT" \ - && echo 'if [ -n "$1" ]; then "$@"; else /usr/bin/env bash; fi' >> "$ND_ENTRYPOINT"; \ - fi \ - && chmod -R 777 /neurodocker && chmod a+s /neurodocker -RUN apt-get update -qq \ - && apt-get install -y -q --no-install-recommends \ - build-essential \ - curl \ - gnupg \ - less \ - libasound2-dev \ - libgtk-3-dev \ - libusb-1.0-0-dev \ - libwxgtk-media3.2-dev \ - libwxgtk-webview3.2-dev \ - libwxgtk3.2-dev \ - ncdu \ - pigz \ - pkg-config \ - portaudio19-dev \ - procps \ - python3 \ - python3-pip \ - strace \ - time \ - tree \ - vim \ - wget \ - && rm -rf /var/lib/apt/lists/* -ENV CONDA_DIR="/opt/miniconda-py311_24.5.0-0" \ - PATH="/opt/miniconda-py311_24.5.0-0/bin:$PATH" -RUN apt-get update -qq \ - && apt-get install -y -q --no-install-recommends \ - bzip2 \ - ca-certificates \ - curl \ - && rm -rf /var/lib/apt/lists/* \ - # Install dependencies. - && export PATH="/opt/miniconda-py311_24.5.0-0/bin:$PATH" \ - && echo "Downloading Miniconda installer ..." \ - && conda_installer="/tmp/miniconda.sh" \ - && curl -fsSL -o "$conda_installer" https://repo.continuum.io/miniconda/Miniconda3-py311_24.5.0-0-Linux-x86_64.sh \ - && bash "$conda_installer" -b -p /opt/miniconda-py311_24.5.0-0 \ - && rm -f "$conda_installer" \ - # Prefer packages in conda-forge - && conda config --system --prepend channels conda-forge \ - # Packages in lower-priority channels not considered if a package with the same - # name exists in a higher priority channel. Can dramatically speed up installations. - # Conda recommends this as a default - # https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-channels.html - && conda config --set channel_priority strict \ - && conda config --system --set auto_update_conda false \ - && conda config --system --set show_channel_urls true \ - # Enable `conda activate` - && conda init bash \ - && conda install -y --name base \ - "conda-forge::qrcode" \ - && bash -c "source activate base \ - && python -m pip install --no-cache-dir \ - "psychopy" \ - "psychtoolbox"" \ - # Clean up - && sync && conda clean --all --yes && sync \ - && rm -rf ~/.cache/pip/* -RUN test "$(getent passwd reproin)" \ - || useradd --no-user-group --create-home --shell /bin/bash reproin -USER reproin -ENTRYPOINT ["/neurodocker/startup.sh"] - -# Save specification to JSON. -USER root -RUN printf '{ \ - "pkg_manager": "apt", \ - "existing_users": [ \ - "root" \ - ], \ - "instructions": [ \ - { \ - "name": "from_", \ - "kwds": { \ - "base_image": "neurodebian:bookworm" \ - } \ - }, \ - { \ - "name": "env", \ - "kwds": { \ - "LANG": "en_US.UTF-8", \ - "LC_ALL": "en_US.UTF-8", \ - "ND_ENTRYPOINT": "/neurodocker/startup.sh" \ - } \ - }, \ - { \ - "name": "run", \ - "kwds": { \ - "command": "export ND_ENTRYPOINT=\\"/neurodocker/startup.sh\\"\\napt-get update -qq\\napt-get install -y -q --no-install-recommends \\\\\\n apt-utils \\\\\\n bzip2 \\\\\\n ca-certificates \\\\\\n curl \\\\\\n locales \\\\\\n unzip\\nrm -rf /var/lib/apt/lists/*\\nsed -i -e '"'"'s/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/'"'"' /etc/locale.gen\\ndpkg-reconfigure --frontend=noninteractive locales\\nupdate-locale LANG=\\"en_US.UTF-8\\"\\nchmod 777 /opt && chmod a+s /opt\\nmkdir -p /neurodocker\\nif [ ! -f \\"$ND_ENTRYPOINT\\" ]; then\\n echo '"'"'#!/usr/bin/env bash'"'"' >> \\"$ND_ENTRYPOINT\\"\\n echo '"'"'set -e'"'"' >> \\"$ND_ENTRYPOINT\\"\\n echo '"'"'export USER=\\"${USER:=`whoami`}\\"'"'"' >> \\"$ND_ENTRYPOINT\\"\\n echo '"'"'if [ -n \\"$1\\" ]; then \\"$@\\"; else /usr/bin/env bash; fi'"'"' >> \\"$ND_ENTRYPOINT\\";\\nfi\\nchmod -R 777 /neurodocker && chmod a+s /neurodocker" \ - } \ - }, \ - { \ - "name": "install", \ - "kwds": { \ - "pkgs": [ \ - "build-essential", \ - "pkg-config", \ - "libgtk-3-dev", \ - "libwxgtk3.2-dev", \ - "libwxgtk-media3.2-dev", \ - "libwxgtk-webview3.2-dev", \ - "libusb-1.0-0-dev", \ - "portaudio19-dev", \ - "libasound2-dev", \ - "vim", \ - "wget", \ - "strace", \ - "time", \ - "ncdu", \ - "gnupg", \ - "curl", \ - "procps", \ - "pigz", \ - "less", \ - "tree", \ - "python3", \ - "python3-pip" \ - ], \ - "opts": null \ - } \ - }, \ - { \ - "name": "run", \ - "kwds": { \ - "command": "apt-get update -qq \\\\\\n && apt-get install -y -q --no-install-recommends \\\\\\n build-essential \\\\\\n curl \\\\\\n gnupg \\\\\\n less \\\\\\n libasound2-dev \\\\\\n libgtk-3-dev \\\\\\n libusb-1.0-0-dev \\\\\\n libwxgtk-media3.2-dev \\\\\\n libwxgtk-webview3.2-dev \\\\\\n libwxgtk3.2-dev \\\\\\n ncdu \\\\\\n pigz \\\\\\n pkg-config \\\\\\n portaudio19-dev \\\\\\n procps \\\\\\n python3 \\\\\\n python3-pip \\\\\\n strace \\\\\\n time \\\\\\n tree \\\\\\n vim \\\\\\n wget \\\\\\n && rm -rf /var/lib/apt/lists/*" \ - } \ - }, \ - { \ - "name": "env", \ - "kwds": { \ - "CONDA_DIR": "/opt/miniconda-py311_24.5.0-0", \ - "PATH": "/opt/miniconda-py311_24.5.0-0/bin:$PATH" \ - } \ - }, \ - { \ - "name": "run", \ - "kwds": { \ - "command": "apt-get update -qq\\napt-get install -y -q --no-install-recommends \\\\\\n bzip2 \\\\\\n ca-certificates \\\\\\n curl\\nrm -rf /var/lib/apt/lists/*\\n# Install dependencies.\\nexport PATH=\\"/opt/miniconda-py311_24.5.0-0/bin:$PATH\\"\\necho \\"Downloading Miniconda installer ...\\"\\nconda_installer=\\"/tmp/miniconda.sh\\"\\ncurl -fsSL -o \\"$conda_installer\\" https://repo.continuum.io/miniconda/Miniconda3-py311_24.5.0-0-Linux-x86_64.sh\\nbash \\"$conda_installer\\" -b -p /opt/miniconda-py311_24.5.0-0\\nrm -f \\"$conda_installer\\"\\n# Prefer packages in conda-forge\\nconda config --system --prepend channels conda-forge\\n# Packages in lower-priority channels not considered if a package with the same\\n# name exists in a higher priority channel. Can dramatically speed up installations.\\n# Conda recommends this as a default\\n# https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-channels.html\\nconda config --set channel_priority strict\\nconda config --system --set auto_update_conda false\\nconda config --system --set show_channel_urls true\\n# Enable `conda activate`\\nconda init bash\\nconda install -y --name base \\\\\\n \\"conda-forge::qrcode\\"\\nbash -c \\"source activate base\\n python -m pip install --no-cache-dir \\\\\\n \\"psychopy\\" \\\\\\n \\"psychtoolbox\\"\\"\\n# Clean up\\nsync && conda clean --all --yes && sync\\nrm -rf ~/.cache/pip/*" \ - } \ - }, \ - { \ - "name": "user", \ - "kwds": { \ - "user": "reproin" \ - } \ - }, \ - { \ - "name": "entrypoint", \ - "kwds": { \ - "args": [ \ - "/neurodocker/startup.sh" \ - ] \ - } \ - } \ - ] \ -}' > /.reproenv.json -USER reproin -# End saving to specification to JSON. diff --git a/containers/reprostim-timesync/Singularity b/containers/reprostim-timesync/Singularity deleted file mode 100644 index dec372c..0000000 --- a/containers/reprostim-timesync/Singularity +++ /dev/null @@ -1,200 +0,0 @@ -# Generated by Neurodocker and Reproenv. - -Bootstrap: docker -From: neurodebian:bookworm - -%environment -export LANG="en_US.UTF-8" -export LC_ALL="en_US.UTF-8" -export ND_ENTRYPOINT="/neurodocker/startup.sh" -export CONDA_DIR="/opt/miniconda-py311_24.5.0-0" -export PATH="/opt/miniconda-py311_24.5.0-0/bin:$PATH" - -%post -export ND_ENTRYPOINT="/neurodocker/startup.sh" -apt-get update -qq -apt-get install -y -q --no-install-recommends \ - apt-utils \ - bzip2 \ - ca-certificates \ - curl \ - locales \ - unzip -rm -rf /var/lib/apt/lists/* -sed -i -e 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen -dpkg-reconfigure --frontend=noninteractive locales -update-locale LANG="en_US.UTF-8" -chmod 777 /opt && chmod a+s /opt -mkdir -p /neurodocker -if [ ! -f "$ND_ENTRYPOINT" ]; then - echo '#!/usr/bin/env bash' >> "$ND_ENTRYPOINT" - echo 'set -e' >> "$ND_ENTRYPOINT" - echo 'export USER="${USER:=`whoami`}"' >> "$ND_ENTRYPOINT" - echo 'if [ -n "$1" ]; then "$@"; else /usr/bin/env bash; fi' >> "$ND_ENTRYPOINT"; -fi -chmod -R 777 /neurodocker && chmod a+s /neurodocker - -apt-get update -qq -apt-get install -y -q --no-install-recommends \ - build-essential \ - curl \ - gnupg \ - less \ - libasound2-dev \ - libgtk-3-dev \ - libusb-1.0-0-dev \ - libwxgtk-media3.2-dev \ - libwxgtk-webview3.2-dev \ - libwxgtk3.2-dev \ - ncdu \ - pigz \ - pkg-config \ - portaudio19-dev \ - procps \ - python3 \ - python3-pip \ - strace \ - time \ - tree \ - vim \ - wget -rm -rf /var/lib/apt/lists/* - -apt-get update -qq -apt-get install -y -q --no-install-recommends \ - bzip2 \ - ca-certificates \ - curl -rm -rf /var/lib/apt/lists/* -# Install dependencies. -export PATH="/opt/miniconda-py311_24.5.0-0/bin:$PATH" -echo "Downloading Miniconda installer ..." -conda_installer="/tmp/miniconda.sh" -curl -fsSL -o "$conda_installer" https://repo.continuum.io/miniconda/Miniconda3-py311_24.5.0-0-Linux-x86_64.sh -bash "$conda_installer" -b -p /opt/miniconda-py311_24.5.0-0 -rm -f "$conda_installer" -# Prefer packages in conda-forge -conda config --system --prepend channels conda-forge -# Packages in lower-priority channels not considered if a package with the same -# name exists in a higher priority channel. Can dramatically speed up installations. -# Conda recommends this as a default -# https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-channels.html -conda config --set channel_priority strict -conda config --system --set auto_update_conda false -conda config --system --set show_channel_urls true -# Enable `conda activate` -conda init bash -conda install -y --name base \ - "conda-forge::qrcode" -bash -c "source activate base - python -m pip install --no-cache-dir \ - "psychopy" \ - "psychtoolbox"" -# Clean up -sync && conda clean --all --yes && sync -rm -rf ~/.cache/pip/* - -test "$(getent passwd reproin)" \ -|| useradd --no-user-group --create-home --shell /bin/bash reproin - - -su - reproin - -# Save specification to JSON. -su - root -printf '{ \ - "pkg_manager": "apt", \ - "existing_users": [ \ - "root" \ - ], \ - "instructions": [ \ - { \ - "name": "from_", \ - "kwds": { \ - "base_image": "neurodebian:bookworm" \ - } \ - }, \ - { \ - "name": "env", \ - "kwds": { \ - "LANG": "en_US.UTF-8", \ - "LC_ALL": "en_US.UTF-8", \ - "ND_ENTRYPOINT": "/neurodocker/startup.sh" \ - } \ - }, \ - { \ - "name": "run", \ - "kwds": { \ - "command": "export ND_ENTRYPOINT=\\"/neurodocker/startup.sh\\"\\napt-get update -qq\\napt-get install -y -q --no-install-recommends \\\\\\n apt-utils \\\\\\n bzip2 \\\\\\n ca-certificates \\\\\\n curl \\\\\\n locales \\\\\\n unzip\\nrm -rf /var/lib/apt/lists/*\\nsed -i -e '"'"'s/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/'"'"' /etc/locale.gen\\ndpkg-reconfigure --frontend=noninteractive locales\\nupdate-locale LANG=\\"en_US.UTF-8\\"\\nchmod 777 /opt && chmod a+s /opt\\nmkdir -p /neurodocker\\nif [ ! -f \\"$ND_ENTRYPOINT\\" ]; then\\n echo '"'"'#!/usr/bin/env bash'"'"' >> \\"$ND_ENTRYPOINT\\"\\n echo '"'"'set -e'"'"' >> \\"$ND_ENTRYPOINT\\"\\n echo '"'"'export USER=\\"${USER:=`whoami`}\\"'"'"' >> \\"$ND_ENTRYPOINT\\"\\n echo '"'"'if [ -n \\"$1\\" ]; then \\"$@\\"; else /usr/bin/env bash; fi'"'"' >> \\"$ND_ENTRYPOINT\\";\\nfi\\nchmod -R 777 /neurodocker && chmod a+s /neurodocker" \ - } \ - }, \ - { \ - "name": "install", \ - "kwds": { \ - "pkgs": [ \ - "build-essential", \ - "pkg-config", \ - "libgtk-3-dev", \ - "libwxgtk3.2-dev", \ - "libwxgtk-media3.2-dev", \ - "libwxgtk-webview3.2-dev", \ - "libusb-1.0-0-dev", \ - "portaudio19-dev", \ - "libasound2-dev", \ - "vim", \ - "wget", \ - "strace", \ - "time", \ - "ncdu", \ - "gnupg", \ - "curl", \ - "procps", \ - "pigz", \ - "less", \ - "tree", \ - "python3", \ - "python3-pip" \ - ], \ - "opts": null \ - } \ - }, \ - { \ - "name": "run", \ - "kwds": { \ - "command": "apt-get update -qq\\napt-get install -y -q --no-install-recommends \\\\\\n build-essential \\\\\\n curl \\\\\\n gnupg \\\\\\n less \\\\\\n libasound2-dev \\\\\\n libgtk-3-dev \\\\\\n libusb-1.0-0-dev \\\\\\n libwxgtk-media3.2-dev \\\\\\n libwxgtk-webview3.2-dev \\\\\\n libwxgtk3.2-dev \\\\\\n ncdu \\\\\\n pigz \\\\\\n pkg-config \\\\\\n portaudio19-dev \\\\\\n procps \\\\\\n python3 \\\\\\n python3-pip \\\\\\n strace \\\\\\n time \\\\\\n tree \\\\\\n vim \\\\\\n wget\\nrm -rf /var/lib/apt/lists/*" \ - } \ - }, \ - { \ - "name": "env", \ - "kwds": { \ - "CONDA_DIR": "/opt/miniconda-py311_24.5.0-0", \ - "PATH": "/opt/miniconda-py311_24.5.0-0/bin:$PATH" \ - } \ - }, \ - { \ - "name": "run", \ - "kwds": { \ - "command": "apt-get update -qq\\napt-get install -y -q --no-install-recommends \\\\\\n bzip2 \\\\\\n ca-certificates \\\\\\n curl\\nrm -rf /var/lib/apt/lists/*\\n# Install dependencies.\\nexport PATH=\\"/opt/miniconda-py311_24.5.0-0/bin:$PATH\\"\\necho \\"Downloading Miniconda installer ...\\"\\nconda_installer=\\"/tmp/miniconda.sh\\"\\ncurl -fsSL -o \\"$conda_installer\\" https://repo.continuum.io/miniconda/Miniconda3-py311_24.5.0-0-Linux-x86_64.sh\\nbash \\"$conda_installer\\" -b -p /opt/miniconda-py311_24.5.0-0\\nrm -f \\"$conda_installer\\"\\n# Prefer packages in conda-forge\\nconda config --system --prepend channels conda-forge\\n# Packages in lower-priority channels not considered if a package with the same\\n# name exists in a higher priority channel. Can dramatically speed up installations.\\n# Conda recommends this as a default\\n# https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-channels.html\\nconda config --set channel_priority strict\\nconda config --system --set auto_update_conda false\\nconda config --system --set show_channel_urls true\\n# Enable `conda activate`\\nconda init bash\\nconda install -y --name base \\\\\\n \\"conda-forge::qrcode\\"\\nbash -c \\"source activate base\\n python -m pip install --no-cache-dir \\\\\\n \\"psychopy\\" \\\\\\n \\"psychtoolbox\\"\\"\\n# Clean up\\nsync && conda clean --all --yes && sync\\nrm -rf ~/.cache/pip/*" \ - } \ - }, \ - { \ - "name": "user", \ - "kwds": { \ - "user": "reproin" \ - } \ - }, \ - { \ - "name": "entrypoint", \ - "kwds": { \ - "args": [ \ - "/neurodocker/startup.sh" \ - ] \ - } \ - } \ - ] \ -}' > /.reproenv.json -su - reproin -# End saving to specification to JSON. - -%runscript -/neurodocker/startup.sh diff --git a/containers/reprostim-timesync/generate_container.sh b/containers/reprostim-timesync/generate_container.sh deleted file mode 100755 index f87b786..0000000 --- a/containers/reprostim-timesync/generate_container.sh +++ /dev/null @@ -1,39 +0,0 @@ -#!/bin/bash - -set -eu - -generate() { - # more details might come on https://github.com/ReproNim/neurodocker/issues/330 - [ "$1" == singularity ] && add_entry=' "$@"' || add_entry='' - #neurodocker generate "$1" \ - ndversion=1.0.1 - #ndversion=master - #--ndfreeze date=20240801 \ - # Thought to use conda-forge for this, but feedstock is not maintained: - # https://github.com/conda-forge/psychopy-feedstock/issues/64 - # --miniconda version=py312_24.5.0-0 conda_install="conda-forge::psychopy conda-forge::qrcode" \ - # Had to go with 3.11 due to https://stackoverflow.com/questions/77364550/attributeerror-module-pkgutil-has-no-attribute-impimporter-did-you-mean - # Need extra -dev libraries etc to install/build wxpython - docker run --rm repronim/neurodocker:$ndversion generate "$1" \ - --base-image=neurodebian:bookworm \ - --pkg-manager=apt \ - --install build-essential pkg-config \ - libgtk-3-dev libwxgtk3.2-dev libwxgtk-media3.2-dev libwxgtk-webview3.2-dev libcanberra-gtk3-module \ - libusb-1.0-0-dev portaudio19-dev libasound2-dev \ - vim wget strace time ncdu gnupg curl procps pigz less tree python3 python3-pip \ - --miniconda version=py311_24.5.0-0 conda_install="conda-forge::qrcode" pip_install="psychopy psychtoolbox" \ - --user=reproin \ -# \ -# --run "$run_cmd" \ -# --run "apt-get update && apt-get -y dist-upgrade" \ -# --run "curl -sL https://deb.nodesource.com/setup_20.x | bash - " \ -# --install nodejs \ -# --run "npm install -g bids-validator@1.14.5" \ -# --run "mkdir /afs /inbox" \ -# --copy bin/reproin /usr/local/bin/reproin \ -# --run "chmod a+rx /usr/local/bin/reproin" \ -# --entrypoint "/usr/local/bin/reproin$add_entry" -} - -generate docker > Dockerfile -generate singularity > Singularity diff --git a/containers/reprostim-timesync-2/Dockerfile b/containers/reprostim-timesync/reprostim-timesync-2/Dockerfile similarity index 100% rename from containers/reprostim-timesync-2/Dockerfile rename to containers/reprostim-timesync/reprostim-timesync-2/Dockerfile diff --git a/containers/reprostim-timesync-2/Singularity b/containers/reprostim-timesync/reprostim-timesync-2/Singularity similarity index 100% rename from containers/reprostim-timesync-2/Singularity rename to containers/reprostim-timesync/reprostim-timesync-2/Singularity diff --git a/containers/reprostim-timesync-2/generate_container.sh b/containers/reprostim-timesync/reprostim-timesync-2/generate_container.sh similarity index 100% rename from containers/reprostim-timesync-2/generate_container.sh rename to containers/reprostim-timesync/reprostim-timesync-2/generate_container.sh