Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

[ENH] Update Dockerfile #3039

Merged
merged 4 commits into from
Nov 26, 2024
Merged

[ENH] Update Dockerfile #3039

Changes from 3 commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
a8cb9c1
update dockerfile without slim and eddyqc fix
arnaudbore Nov 20, 2024
9511d7e
Merge branch 'master' into update_docker
arnaudbore Nov 20, 2024
6249ad2
restore slim version and add procps
arnaudbore Nov 21, 2024
04699ce
merge master
arnaudbore Nov 26, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
27 changes: 16 additions & 11 deletions Dockerfile
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@ ARG MAKE_JOBS="1"
ARG DEBIAN_FRONTEND="noninteractive"

FROM python:3.8-slim AS base
FROM buildpack-deps:buster AS base-builder
FROM buildpack-deps:bookworm AS base-builder

FROM base-builder AS mrtrix3-builder

Expand All @@ -22,16 +22,17 @@ RUN apt-get -qq update \
libqt5opengl5-dev \
libqt5svg5-dev \
libtiff5-dev \
qt5-default \
python3 \
qtbase5-dev \
zlib1g-dev \
&& rm -rf /var/lib/apt/lists/*

# Clone, build, and install MRtrix3.
ARG MAKE_JOBS
WORKDIR /opt/mrtrix3
RUN git clone -b $MRTRIX3_GIT_COMMITISH --depth 1 https://github.com/MRtrix3/mrtrix3.git . \
&& ./configure $MRTRIX3_CONFIGURE_FLAGS \
&& NUMBER_OF_PROCESSORS=$MAKE_JOBS ./build $MRTRIX3_BUILD_FLAGS \
&& python3 ./configure $MRTRIX3_CONFIGURE_FLAGS \
&& NUMBER_OF_PROCESSORS=$MAKE_JOBS python3 ./build $MRTRIX3_BUILD_FLAGS \
&& rm -rf tmp

# Download minified ART ACPCdetect (V2.0).
Expand All @@ -51,10 +52,10 @@ FROM base-builder as freesurfer-installer
WORKDIR /opt/freesurfer
RUN curl -fsSLO https://raw.githubusercontent.com/freesurfer/freesurfer/v7.1.1/distribution/FreeSurferColorLUT.txt

# Download minified FSL (6.0.4-2)
# Download minified FSL (6.0.7.7)
FROM base-builder as fsl-installer
WORKDIR /opt/fsl
RUN curl -fsSL https://osf.io/dtep4/download \
RUN curl -fsSL https://osf.io/ph9ex/download \
| tar xz --strip-components 1

# Build final image.
Expand All @@ -66,7 +67,8 @@ RUN apt-get -qq update \
binutils \
dc \
less \
libfftw3-3 \
libfftw3-single3 \
libfftw3-double3 \
libgl1-mesa-glx \
libgomp1 \
liblapack3 \
Expand All @@ -77,8 +79,10 @@ RUN apt-get -qq update \
libqt5svg5 \
libqt5widgets5 \
libquadmath0 \
libtiff5 \
libtiff5-dev \
python3 \
python3-distutils \
procps \
&& rm -rf /var/lib/apt/lists/*

COPY --from=acpcdetect-installer /opt/art /opt/art
Expand All @@ -95,12 +99,13 @@ ENV ANTSPATH="/opt/ants/bin" \
FSLMULTIFILEQUIT="TRUE" \
FSLTCLSH="/opt/fsl/bin/fsltclsh" \
FSLWISH="/opt/fsl/bin/fslwish" \
LD_LIBRARY_PATH="/opt/fsl/lib:$LD_LIBRARY_PATH" \
PATH="/opt/mrtrix3/bin:/opt/ants/bin:/opt/art/bin:/opt/fsl/bin:$PATH"
PATH="/opt/mrtrix3/bin:/opt/ants/bin:/opt/art/bin:/opt/fsl/share/fsl/bin:$PATH"

# Fix "Singularity container cannot load libQt5Core.so.5" on CentOS 7
RUN strip --remove-section=.note.ABI-tag /usr/lib/x86_64-linux-gnu/libQt5Core.so.5 \
&& ldconfig \
&& apt-get purge -yq binutils

CMD ["/bin/bash"]
RUN ln -s /usr/bin/python3 /usr/bin/python

CMD ["/bin/bash"]