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Merged
merged 4 commits into from
Jan 30, 2023
Merged

MNT: Upgrade Docker base, c3d #275

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12ff481
MNT: Upgrade Docker base, c3d
mgxd Jan 30, 2023
52e27f5
MNT: Clean up dockerfile
mgxd Jan 30, 2023
221c0dc
FIX: Use unknown version if not found
mgxd Jan 30, 2023
be43ddb
DKR: Ensure /home/nibabies is fully available
mgxd Jan 30, 2023
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49 changes: 25 additions & 24 deletions Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@ COPY . /src/nibabies
RUN python -m build /src/nibabies

# Ubuntu 20.04 LTS
FROM ubuntu:focal-20221130
FROM ubuntu:jammy-20221130
ENV DEBIAN_FRONTEND="noninteractive" \
LANG="en_US.UTF-8" \
LC_ALL="en_US.UTF-8"
Expand All @@ -22,12 +22,11 @@ RUN apt-get update && \
ca-certificates \
curl \
git \
graphviz \
gnupg \
libtool \
locales \
lsb-release \
pandoc \
pandoc-citeproc \
netbase \
pkg-config \
unzip \
xvfb && \
Expand All @@ -44,6 +43,9 @@ WORKDIR $ANTSPATH
RUN curl -sSL "https://dl.dropbox.com/s/gwf51ykkk5bifyj/ants-Linux-centos6_x86_64-v2.3.4.tar.gz" \
| tar -xzC $ANTSPATH --strip-components 1

RUN GNUPGHOME=/tmp gpg --keyserver hkps://keyserver.ubuntu.com --no-default-keyring --keyring /usr/share/keyrings/linuxuprising.gpg --recv 0xEA8CACC073C3DB2A \
&& echo "deb [signed-by=/usr/share/keyrings/linuxuprising.gpg] https://ppa.launchpadcontent.net/linuxuprising/libpng12/ubuntu jammy main" > /etc/apt/sources.list.d/linuxuprising.list

# # AFNI latest (neurodocker build)
RUN apt-get update -qq \
&& apt-get install -y -q --no-install-recommends \
Expand All @@ -54,6 +56,7 @@ RUN apt-get update -qq \
libglw1-mesa \
libgomp1 \
libjpeg62 \
libpng12-0 \
libxm4 \
netpbm \
tcsh \
Expand All @@ -67,9 +70,6 @@ RUN apt-get update -qq \
&& curl -sSL --retry 5 -o /tmp/libxp6.deb http://mirrors.kernel.org/debian/pool/main/libx/libxp/libxp6_1.0.2-2_amd64.deb \
&& dpkg -i /tmp/libxp6.deb \
&& rm /tmp/libxp6.deb \
&& curl -sSL --retry 5 -o /tmp/libpng.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/libpng.deb \
&& rm /tmp/libpng.deb \
&& apt-get install -f \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/* \
Expand Down Expand Up @@ -111,16 +111,6 @@ RUN echo "Downloading AFNI ..." \
-name "3dAutomask" -or \
-name "3dvolreg" \) -delete

# Convert3D (neurodocker build)
RUN echo "Downloading Convert3D ..." \
&& mkdir -p /opt/convert3d-1.0.0 \
&& curl -fsSL --retry 5 https://sourceforge.net/projects/c3d/files/c3d/1.0.0/c3d-1.0.0-Linux-x86_64.tar.gz/download \
| tar -xz -C /opt/convert3d-1.0.0 --strip-components 1 \
--exclude "c3d-1.0.0-Linux-x86_64/lib" \
--exclude "c3d-1.0.0-Linux-x86_64/share" \
--exclude "c3d-1.0.0-Linux-x86_64/bin/c3d_gui"
ENV C3DPATH="/opt/convert3d-1.0.0" \
PATH="/opt/convert3d-1.0.0/bin:$PATH"

# FSL 6.0.5.1
RUN apt-get update -qq \
Expand Down Expand Up @@ -213,7 +203,8 @@ ENV SUBJECTS_DIR="$FREESURFER_HOME/subjects" \
MINC_BIN_DIR="$FREESURFER_HOME/mni/bin" \
MINC_LIB_DIR="$FREESURFER_HOME/mni/lib" \
MNI_DATAPATH="$FREESURFER_HOME/mni/data" \
FSL_DIR=${FSLDIR}
FSL_DIR=${FSLDIR} \
FREESURFER="/opt/freesurfer"
ENV PERL5LIB="$MINC_LIB_DIR/perl5/5.8.5" \
MNI_PERL5LIB="$MINC_LIB_DIR/perl5/5.8.5" \
PATH="$FREESURFER_HOME/bin:$FREESURFER_HOME/tktools:$MINC_BIN_DIR:$PATH"
Expand Down Expand Up @@ -242,16 +233,17 @@ ENV PATH="/opt/ICA-AROMA:$PATH" \
AROMA_VERSION="0.4.5"

# Create a shared $HOME directory
RUN useradd -m -s /bin/bash -G users nibabies
RUN useradd -m -s /bin/bash -G users nibabies && chmod -R 777 /home/nibabies
WORKDIR /home/nibabies
ENV HOME="/home/nibabies"
ENV HOME="/home/nibabies" \
LD_LIBRARY_PATH="/usr/lib/x86_64-linux-gnu:${LD_LIBRARY_PATH}"

# py39_2209.01
COPY --from=nipreps/miniconda@sha256:8894ca17e3c8ba963812a6876093463eab6b88871bcfe23f71ebc84cf38451db /opt/conda /opt/conda

RUN ln -s /opt/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh && \
echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc && \
echo "conda activate base" >> ~/.bashrc
echo ". /opt/conda/etc/profile.d/conda.sh" >> ${HOME}/.bashrc && \
echo "conda activate base" >> ${HOME}/.bashrc

# Set CPATH for packages relying on compiled libs (e.g. indexed_gzip)
ENV PATH="/opt/conda/bin:$PATH" \
Expand All @@ -262,10 +254,19 @@ ENV PATH="/opt/conda/bin:$PATH" \
IS_DOCKER_8395080871=1 \
CONDA_PYTHON="/opt/conda/bin/python"

# Convert3d
RUN conda install -y -n base \
-c anaconda \
-c conda-forge \
convert3d=1.3.0 \
&& sync \
&& conda clean -afy; sync \
&& rm -rf ~/.conda ~/.cache/pip/*; sync \
&& ldconfig

# Precaching atlases
COPY scripts/fetch_templates.py fetch_templates.py
RUN ${CONDA_PYTHON} -m pip install --no-cache-dir templateflow && \
${CONDA_PYTHON} fetch_templates.py && \
RUN ${CONDA_PYTHON} fetch_templates.py && \
rm fetch_templates.py && \
find $HOME/.cache/templateflow -type d -exec chmod go=u {} + && \
find $HOME/.cache/templateflow -type f -exec chmod go=u {} +
Expand Down
2 changes: 1 addition & 1 deletion nibabies/__about__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@
try:
from ._version import __version__
except ImportError:
__version__ == "0+unknown"
__version__ = "0+unknown"

__org__ = "nipreps"
__packagename__ = "nibabies"
Expand Down