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@bclenet
bclenet committed Nov 21, 2024
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2 changes: 1 addition & 1 deletion CONTENT.md
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### Contents overview
# Contents overview

- :snake: :package: `narps_open/` contains the Python package with all the pipelines logic.
- :brain: `data/` contains data that is used by the pipelines, as well as the (intermediate or final) results data. Instructions to download data are available in [INSTALL.md](/INSTALL.md#data-download-instructions).
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321 changes: 5 additions & 316 deletions Dockerfile
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# Generated by: Neurodocker version 0.7.0+0.gdc97516.dirty
# Latest release: Neurodocker version 0.7.0
# Timestamp: 2021/11/09 11:04:47 UTC
#
# Thank you for using Neurodocker. If you discover any issues
# or ways to improve this software, please submit an issue or
# pull request on our GitHub repository:
#
# https://github.com/ReproNim/neurodocker
FROM nipype/nipype:py38

FROM neurodebian:stretch-non-free
WORKDIR /work

USER root
COPY narps_open/ ./narps_open/
COPY setup.py ./

ARG DEBIAN_FRONTEND="noninteractive"

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 \
&& apt-get clean \
&& 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

ENTRYPOINT ["/neurodocker/startup.sh"]

RUN apt-get update -qq \
&& apt-get install -y -q --no-install-recommends \
git \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/*

ENV FSLDIR="/opt/fsl-6.0.3" \
PATH="/opt/fsl-6.0.3/bin:$PATH" \
FSLOUTPUTTYPE="NIFTI_GZ" \
FSLMULTIFILEQUIT="TRUE" \
FSLTCLSH="/opt/fsl-6.0.3/bin/fsltclsh" \
FSLWISH="/opt/fsl-6.0.3/bin/fslwish" \
FSLLOCKDIR="" \
FSLMACHINELIST="" \
FSLREMOTECALL="" \
FSLGECUDAQ="cuda.q"
RUN apt-get update -qq \
&& apt-get install -y -q --no-install-recommends \
bc \
dc \
file \
libfontconfig1 \
libfreetype6 \
libgl1-mesa-dev \
libgl1-mesa-dri \
libglu1-mesa-dev \
libgomp1 \
libice6 \
libxcursor1 \
libxft2 \
libxinerama1 \
libxrandr2 \
libxrender1 \
libxt6 \
sudo \
wget \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/* \
&& echo "Downloading FSL ..." \
&& mkdir -p /opt/fsl-6.0.3 \
&& curl -fsSL --retry 5 https://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-6.0.3-centos6_64.tar.gz \
| tar -xz -C /opt/fsl-6.0.3 --strip-components 1 \
&& sed -i '$iecho Some packages in this Docker container are non-free' $ND_ENTRYPOINT \
&& sed -i '$iecho If you are considering commercial use of this container, please consult the relevant license:' $ND_ENTRYPOINT \
&& sed -i '$iecho https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Licence' $ND_ENTRYPOINT \
&& sed -i '$isource $FSLDIR/etc/fslconf/fsl.sh' $ND_ENTRYPOINT \
&& echo "Installing FSL conda environment ..." \
&& bash /opt/fsl-6.0.3/etc/fslconf/fslpython_install.sh -f /opt/fsl-6.0.3

ENV PATH="/opt/afni-latest:$PATH" \
AFNI_PLUGINPATH="/opt/afni-latest"
RUN apt-get update -qq \
&& apt-get install -y -q --no-install-recommends \
ed \
gsl-bin \
libglib2.0-0 \
libglu1-mesa-dev \
libglw1-mesa \
libgomp1 \
libjpeg62 \
libnlopt-dev \
libxm4 \
netpbm \
python \
python3 \
r-base \
r-base-dev \
tcsh \
xfonts-base \
xvfb \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/* \
&& curl -sSL --retry 5 -o /tmp/toinstall.deb http://mirrors.kernel.org/debian/pool/main/libx/libxp/libxp6_1.0.2-2_amd64.deb \
&& dpkg -i /tmp/toinstall.deb \
&& rm /tmp/toinstall.deb \
&& curl -sSL --retry 5 -o /tmp/toinstall.deb http://snapshot.debian.org/archive/debian-security/20160113T213056Z/pool/updates/main/libp/libpng/libpng12-0_1.2.49-1%2Bdeb7u2_amd64.deb \
&& dpkg -i /tmp/toinstall.deb \
&& rm /tmp/toinstall.deb \
&& apt-get install -f \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/* \
&& gsl2_path="$(find / -name 'libgsl.so.19' || printf '')" \
&& if [ -n "$gsl2_path" ]; then \
ln -sfv "$gsl2_path" "$(dirname $gsl2_path)/libgsl.so.0"; \
fi \
&& ldconfig \
&& echo "Downloading AFNI ..." \
&& mkdir -p /opt/afni-latest \
&& curl -fsSL --retry 5 https://afni.nimh.nih.gov/pub/dist/tgz/linux_openmp_64.tgz \
| tar -xz -C /opt/afni-latest --strip-components 1 \
&& PATH=$PATH:/opt/afni-latest rPkgsInstall -pkgs ALL

ENV FORCE_SPMMCR="1" \
SPM_HTML_BROWSER="0" \
LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/lib/x86_64-linux-gnu:/opt/matlabmcr-2010a/v713/runtime/glnxa64:/opt/matlabmcr-2010a/v713/bin/glnxa64:/opt/matlabmcr-2010a/v713/sys/os/glnxa64:/opt/matlabmcr-2010a/v713/extern/bin/glnxa64" \
MATLABCMD="/opt/matlabmcr-2010a/v713/toolbox/matlab"
RUN export TMPDIR="$(mktemp -d)" \
&& apt-get update -qq \
&& apt-get install -y -q --no-install-recommends \
bc \
libncurses5 \
libxext6 \
libxmu6 \
libxpm-dev \
libxt6 \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/* \
&& echo "Downloading MATLAB Compiler Runtime ..." \
&& curl -sSL --retry 5 -o /tmp/toinstall.deb http://mirrors.kernel.org/debian/pool/main/libx/libxp/libxp6_1.0.2-2_amd64.deb \
&& dpkg -i /tmp/toinstall.deb \
&& rm /tmp/toinstall.deb \
&& apt-get install -f \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/* \
&& curl -fsSL --retry 5 -o "$TMPDIR/MCRInstaller.bin" https://dl.dropbox.com/s/zz6me0c3v4yq5fd/MCR_R2010a_glnxa64_installer.bin \
&& chmod +x "$TMPDIR/MCRInstaller.bin" \
&& "$TMPDIR/MCRInstaller.bin" -silent -P installLocation="/opt/matlabmcr-2010a" \
&& rm -rf "$TMPDIR" \
&& unset TMPDIR \
&& echo "Downloading standalone SPM ..." \
&& curl -fsSL --retry 5 -o /tmp/spm12.zip https://www.fil.ion.ucl.ac.uk/spm/download/restricted/utopia/previous/spm12_r7771_R2010a.zip \
&& unzip -q /tmp/spm12.zip -d /tmp \
&& mkdir -p /opt/spm12-r7771 \
&& mv /tmp/spm12/* /opt/spm12-r7771/ \
&& chmod -R 777 /opt/spm12-r7771 \
&& rm -rf /tmp/spm* \
&& /opt/spm12-r7771/run_spm12.sh /opt/matlabmcr-2010a/v713 quit \
&& sed -i '$iexport SPMMCRCMD=\"/opt/spm12-r7771/run_spm12.sh /opt/matlabmcr-2010a/v713 script\"' $ND_ENTRYPOINT

RUN test "$(getent passwd neuro)" || useradd --no-user-group --create-home --shell /bin/bash neuro
USER neuro

WORKDIR /home

ENV CONDA_DIR="/opt/miniconda-latest" \
PATH="/opt/miniconda-latest/bin:$PATH"
RUN export PATH="/opt/miniconda-latest/bin:$PATH" \
&& echo "Downloading Miniconda installer ..." \
&& conda_installer="/tmp/miniconda.sh" \
&& curl -fsSL --retry 5 -o "$conda_installer" https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh \
&& bash "$conda_installer" -b -p /opt/miniconda-latest \
&& rm -f "$conda_installer" \
&& conda update -yq -nbase conda \
&& conda config --system --prepend channels conda-forge \
&& conda config --system --set auto_update_conda false \
&& conda config --system --set show_channel_urls true \
&& sync && conda clean -y --all && sync \
&& conda create -y -q --name neuro \
&& conda install -y -q --name neuro \
"python=3.8" \
"traits" \
"jupyter" \
"nilearn" \
"graphviz" \
"nipype" \
"scikit-image" \
&& sync && conda clean -y --all && sync \
&& bash -c "source activate neuro \
&& pip install --no-cache-dir \
"matplotlib"" \
&& rm -rf ~/.cache/pip/* \
&& sync \
&& sed -i '$isource activate neuro' $ND_ENTRYPOINT

ENV LD_LIBRARY_PATH="/opt/miniconda-latest/envs/neuro:"

RUN bash -c 'source activate neuro'

USER root

RUN chmod 777 -Rf /home

RUN chown -R neuro /home

USER neuro

RUN mkdir -p ~/.jupyter && echo c.NotebookApp.ip = \"0.0.0.0\" > ~/.jupyter/jupyter_notebook_config.py

RUN echo '{ \
\n "pkg_manager": "apt", \
\n "instructions": [ \
\n [ \
\n "base", \
\n "neurodebian:stretch-non-free" \
\n ], \
\n [ \
\n "install", \
\n [ \
\n "git" \
\n ] \
\n ], \
\n [ \
\n "fsl", \
\n { \
\n "version": "6.0.3" \
\n } \
\n ], \
\n [ \
\n "afni", \
\n { \
\n "version": "latest", \
\n "method": "binaries", \
\n "install_r": "true", \
\n "install_r_pkgs": "true", \
\n "install_python2": "true", \
\n "install_python3": "true" \
\n } \
\n ], \
\n [ \
\n "spm12", \
\n { \
\n "version": "r7771", \
\n "method": "binaries" \
\n } \
\n ], \
\n [ \
\n "user", \
\n "neuro" \
\n ], \
\n [ \
\n "workdir", \
\n "/home" \
\n ], \
\n [ \
\n "miniconda", \
\n { \
\n "create_env": "neuro", \
\n "conda_install": [ \
\n "python=3.8", \
\n "traits", \
\n "jupyter", \
\n "nilearn", \
\n "graphviz", \
\n "nipype", \
\n "scikit-image" \
\n ], \
\n "pip_install": [ \
\n "matplotlib" \
\n ], \
\n "activate": true \
\n } \
\n ], \
\n [ \
\n "env", \
\n { \
\n "LD_LIBRARY_PATH": "/opt/miniconda-latest/envs/neuro:" \
\n } \
\n ], \
\n [ \
\n "run_bash", \
\n "source activate neuro" \
\n ], \
\n [ \
\n "user", \
\n "root" \
\n ], \
\n [ \
\n "run", \
\n "chmod 777 -Rf /home" \
\n ], \
\n [ \
\n "run", \
\n "chown -R neuro /home" \
\n ], \
\n [ \
\n "user", \
\n "neuro" \
\n ], \
\n [ \
\n "run", \
\n "mkdir -p ~/.jupyter && echo c.NotebookApp.ip = \\\"0.0.0.0\\\" > ~/.jupyter/jupyter_notebook_config.py" \
\n ] \
\n ] \
\n}' > /neurodocker/neurodocker_specs.json
RUN /neurodocker/startup.sh pip install .
23 changes: 21 additions & 2 deletions docs/environment.md
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Expand Up @@ -19,6 +19,25 @@ docker run -it \
nipype/nipype:py38
```

> [!NOTE]
> The `Dockerfile` available in the root directory of the repository contains a receipe to build a docker image with the project installed, ready to be launched.
> From the root directory:
>
> ```bash
> # Replace IMAGE_NAME in the following command
> docker build -t IMAGE_NAME .
>
> # Check the image was created
> docker images
>
> # Use IMAGE_NAME again to refer to the newly created image
> docker run -it IMAGE_NAME
> ```
> [!TIP]
> Find useful information on the [Docker documentation page](https://docs.docker.com/get-started/). Here is a [cheat sheet with Docker commands](https://docs.docker.com/get-started/docker_cheatsheet.pdf)
## Use Jupyter with the container
If you wish to use [Jupyter](https://jupyter.org/) to run the code, a port forwarding is needed :
Expand All @@ -43,7 +62,7 @@ You can now access Jupyter using the address provided by the command line.
## Create a custom Docker image

The `elodiegermani/open_pipeline` Docker image is based on [Neurodocker](https://github.com/ReproNim/neurodocker). It was created using the following command line :
If you wish to create your own custom environment, make changes to the parameters, software versions, you can build your custom image using [Neurodocker](https://github.com/ReproNim/neurodocker). Generate a Dockerfile using the following command line :

```bash
docker run --rm repronim/neurodocker:0.7.0 generate docker \
Expand All @@ -67,7 +86,7 @@ docker run --rm repronim/neurodocker:0.7.0 generate docker \
--run 'mkdir -p ~/.jupyter && echo c.NotebookApp.ip = \"0.0.0.0\" > ~/.jupyter/jupyter_notebook_config.py' > Dockerfile
```

If you wish to create your own custom environment, make changes to the parameters, and build your custom image from the generated Dockerfile.
And build a new image from the Dockerfile.

```bash
# Replace IMAGE_NAME in the following command
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15 changes: 0 additions & 15 deletions environment.yml
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2 changes: 0 additions & 2 deletions setup.cfg
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