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romainGuietromainGuiet
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Merge pull request #19 from BIOP/update_desktop
biop-desktop to 0.1.0
2 parents ffa1ecb + 5557980 commit e424796

23 files changed

Lines changed: 501 additions & 65 deletions

‎docker/Dockerfile-base‎

Lines changed: 12 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -107,13 +107,24 @@ RUN mkdir -p /home/biop/Desktop && chown -R biop:biop /home/biop/Desktop \
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&& chown -R biop:biop /home/biop \
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&& chmod -R a+rwx /home/biop/
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110-
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#################################################################
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# Install Inkscape
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RUN sudo apt-get update -y \
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&& sudo apt-get install inkscape -y
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#################################################################
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# OpenCL for clij ...
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RUN apt-get update \
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&& apt-get install -y nvidia-opencl-dev \
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&& apt remove -y libnvidia-compute-550-server \
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&& apt-get autoremove --purge \
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&& apt-get clean \
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&& rm -rf /var/lib/apt/lists/* \
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&& rm -rf /tmp/* \
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&& find /var/log -type f -exec cp /dev/null \{\} \;
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#################################################################
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RUN chown -R biop:biop /home/biop/ \
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&& chmod -R a+rwx /home/biop/
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‎docker/Dockerfile-ms‎

Lines changed: 18 additions & 22 deletions
Original file line numberDiff line numberDiff line change
@@ -1,22 +1,23 @@
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ARG BASE_IMAGE=0.0.3
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ARG BASE_IMAGE=0.1.0
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ARG ALIAS=biop/
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# because COPY --from= doesn't support build-arg (https://github.com/docker/for-mac/issues/2155)
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# we can still do a list of all sub-blocks here to be able to use them in the COPY --from=... below
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# base needs to be last, Don't Ask Wky ! (I don't know) ! and it seems it need to be named 'base' , D.A:W.2 ! but it works !
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ARG QUPATH_VERSION=v0.5.1
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ARG QUPATH_VERSION=v0.5.1-01
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ARG ILASTIK_VERSION=1.4.0-gpu
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ARG FIJI_VERSION=20240325
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ARG FIJI_VERSION=20240429
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ARG CELLPOSE_VERSION=2.2.2
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ARG DEVBIO_VERSION=0.10.1
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ARG SAMAPI_VERSION=0.4.0
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ARG EM_VERSION=0.2.3
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ARG EM_VERSION=1.1.0
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ARG STARDIST_VERSION=0.8.5
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ARG ABBA_VERSION=0.8.0
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ARG ABBA_VERSION=0.8.0-01
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ARG CELLPROFILER_VERSION=4.2.6
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ARG INKSCAPE_VERSION=0.0.1
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ARG OMNI_VERSION=1.0.7-dev
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ARG OMNI_VERSION=1.0.7-dev2
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ARG BRAINRENDER_VERSION=0.0.3
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FROM ${ALIAS}biop-qupath:${QUPATH_VERSION} as qupath-image
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FROM ${ALIAS}biop-ilastik:${ILASTIK_VERSION} as ilastik-image
@@ -29,7 +30,8 @@ FROM ${ALIAS}biop-stardist:${STARDIST_VERSION} as stardist-image
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FROM ${ALIAS}biop-abba:${ABBA_VERSION} as abba-image
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FROM ${ALIAS}biop-cellprofiler:${CELLPROFILER_VERSION} as cellprofiler-image
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FROM ${ALIAS}biop-inkscape:${INKSCAPE_VERSION} as inkscape-image
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FROm ${ALIAS}biop-omnipose:${OMNI_VERSION} as omnipose-image
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FROM ${ALIAS}biop-omni:${OMNI_VERSION} as omnipose-image
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FROM ${ALIAS}biop-brainrender:${BRAINRENDER_VERSION} as brainrender-image
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FROM ${ALIAS}biop-vnc-base:${BASE_IMAGE} as base
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@@ -163,8 +165,17 @@ COPY fiji/Fiji_setWrappersPaths.groovy /home/biop/tmp/Fiji_setWrappersPaths.groo
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RUN chown -R biop:biop /home/biop/tmp \
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&& chmod -R a+rwX /home/biop/tmp
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# add brainrender-napari env
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COPY --from=brainrender-image /opt/conda/envs/brainrender /opt/conda/envs/brainrender
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USER biop
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RUN /opt/Fiji.app/ImageJ-linux64 --headless --run /home/biop/tmp/Fiji_setWrappersPaths.groovy
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# download allen_mouse_25um atlas from brainrender-napari
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RUN source activate brainrender \
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&& brainglobe install -a allen_mouse_25um \
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&& conda deactivate
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USER root
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RUN rm -rf /home/biop/tmp
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@@ -195,21 +206,6 @@ COPY --from=omnipose-image /opt/conda/envs/omnipose/ /opt/conda/envs/omnipose/
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# To make the different conda env available in jupyter
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COPY jupyter/kernels/ /home/biop/.local/share/jupyter/kernels/
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#################################################################
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# # Install OpenCL ( for clij ... )
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# Doesn't work (anymore) on local WSL2 but works on runai !!!
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# see https://github.com/NVIDIA/nvidia-container-toolkit/issues/371
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# We move at the end so that we can build a normal version and WSL one without it, as it is not supported anyway.
204-
RUN apt-get update \
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&& apt-get install -y nvidia-opencl-dev \
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&& apt remove -y libnvidia-compute-545 \
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&& apt-get autoremove --purge \
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&& apt-get clean \
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&& rm -rf /var/lib/apt/lists/* \
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&& rm -rf /tmp/* \
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&& find /var/log -type f -exec cp /dev/null \{\} \;
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#################################################################
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# final chown and chmod
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RUN chown -R biop:biop /home/biop/ \

‎docker/QuPath/Dockerfile-qupath‎

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Original file line numberDiff line numberDiff line change
@@ -42,11 +42,11 @@ RUN chown -R biop:biop /opt/QuPath/QuPath_Common_Data_0.5 \
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&& chmod -R a+rwx /opt/QuPath/QuPath_Common_Data_0.5
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# # TODO : discuss if we prepare unzip from zenodo, or if we update when container start via a git pull ... (less good for reproducibility but better to keep scripts up-to-date)
45-
RUN wget -q https://zenodo.org/records/10869324/files/QuPath_Common_Data_0.5.zip?download=1 -O ${TEMP_DIR}/QuPath_Common_Data_0.5.zip
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RUN wget -q https://zenodo.org/records/11091309/files/QuPath_Common_Data_0.5.zip?download=1 -O ${TEMP_DIR}/QuPath_Common_Data_0.5.zip
4646
RUN unzip ${TEMP_DIR}/QuPath_Common_Data_0.5.zip -d /opt/QuPath/QuPath_Common_Data_0.5 \
4747
&& rm ${TEMP_DIR}/QuPath_Common_Data_0.5.zip
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# # Prepare to set QP_prefs
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COPY QuPath/QuPath_setPaths.groovy /home/biop/tmp/QuPath_setPaths.groovy

‎docker/abba/Dockerfile-abba‎

Lines changed: 25 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1,13 +1,15 @@
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# https://docs.nvidia.com/deeplearning/frameworks/pytorch-release-notes/rel-23-07.html
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#FROM superelastix/elastix:5.0.1 as elastix-image
3-
ARG QUPATH_VERSION=v0.5.1
4-
ARG FIJI_VERSION=20240325
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ARG QUPATH_VERSION=v0.5.1-01
4+
ARG FIJI_VERSION=20240429
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ARG DEEPSLICE_VERSION=1.1.5
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ARG BRAINRENDER_VERSION=0.0.3
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ARG ALIAS=biop/
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FROM ${ALIAS}biop-qupath:${QUPATH_VERSION} as qupath-image
910
FROM ${ALIAS}biop-fiji:${FIJI_VERSION} as fiji-image
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FROM ${ALIAS}biop-deepslice:${DEEPSLICE_VERSION} as deepslice-image
12+
FROM ${ALIAS}biop-brainrender:${BRAINRENDER_VERSION} as brainrender-image
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1214
FROM ${ALIAS}biop-vnc-base:0.0.3 as base
1315

@@ -137,6 +139,27 @@ RUN printf '[Desktop Entry]\nVersion=0.8.0\nName=ABBA\nGenericName=ABBA\nX-GNOM
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RUN chown -R biop:biop /opt/Fiji.app/ \
138140
&& chmod -R a+rwX /opt/Fiji.app/
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142+
# install brainrender
143+
COPY --from=brainrender-image /opt/conda/envs/brainrender /opt/conda/envs/brainrender
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146+
USER biop
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148+
# adds brainrender kernel
149+
RUN source activate brainrender \
150+
&& python -m ipykernel install --user --name brainrender --display-name "Python (brainrender)" \
151+
&& conda deactivate
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153+
# download allen_mouse_25um atlas
154+
RUN source activate brainrender \
155+
&& brainglobe install -a allen_mouse_25um \
156+
&& conda deactivate
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USER root
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RUN chmod -R a+rwX /home/biop/ \
161+
&& chown -R biop:biop /home/biop/
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#################################################################
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# Container start
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USER biop

‎docker/brainrender/Dockerfile-brainrender‎

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@@ -1,4 +1,4 @@
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ARG BASE_IMAGE=0.0.3
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ARG BASE_IMAGE=0.1.0
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ARG ALIAS=biop/
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FROM ${ALIAS}biop-vnc-base:${BASE_IMAGE}
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@@ -13,10 +13,12 @@ RUN conda env update -n brainrender -f /tmp/env_brainrender.yml \
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USER biop
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16+
# adds brainrender kernel
1617
RUN source activate brainrender \
1718
&& python -m ipykernel install --user --name brainrender --display-name "Python (brainrender)" \
1819
&& conda deactivate
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21+
# download allen_mouse_25um atlas
2022
RUN source activate brainrender \
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&& brainglobe install -a allen_mouse_25um \
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&& conda deactivate

‎docker/brainrender/env_brainrender.yml‎

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Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
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name: "devbio"
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name: "brainrender-napari"
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channels:
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- conda-forge
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dependencies:
@@ -7,5 +7,6 @@ dependencies:
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- pyqt
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- pip
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- pip :
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- brainrender-napari
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prefix: "/opt/conda/envs/devbio"
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- brainrender-napari==0.0.3
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- bg-atlasapi
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prefix: "/opt/conda/envs/brainrender-napari"

‎docker/celldetection/Dockerfile-celldetection‎

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ARG BASE_IMAGE=0.0.3
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ARG ALIAS=biop/
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4+
5+
FROM ${ALIAS}biop-vnc-base:${BASE_IMAGE}
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7+
8+
USER root
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10+
# install celldetection and download models ( https://celldetection.readthedocs.io/en/latest/models.html )
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COPY celldetection/env_celldetection.yml /tmp/env_celldetection.yml
12+
RUN conda env update -n celldetection -f /tmp/env_celldetection.yml \
13+
&& conda clean --all -f -y \
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&& conda env export -n "biop" \
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&& rm /tmp/env_celldetection.yml
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17+
# get model
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RUN mkdir -p /home/biop/.cache/torch/hub/checkpoints/
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RUN wget https://celldetection.org/torch/models/ginoro_CpnResNeXt101UNet-fbe875f1a3e5ce2c.pt -O /home/biop/.cache/torch/hub/checkpoints/ginoro_CpnResNeXt101UNet-fbe875f1a3e5ce2c.pt
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RUN wget https://celldetection.org/torch/models/.pt -O /home/biop/.cache/torch/hub/checkpoints/.pt
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22+
RUN mkdir -p /home/biop/celldetection/ \
23+
&& chown -R biop:biop /home/biop/ \
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&& chmod -R a+rwX /home/biop/
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26+
COPY celldetection/start_celldetection.sh /opt/celldetection/start_celldetection.sh
27+
COPY napari/napari-icon.ico /opt/celldetection/napari-icon.ico
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29+
RUN printf '[Desktop Entry]\nVersion=0.0.1\nName=celldetection\nGenericName=celldetection\nX-GNOME-FullName=celldetection\nComment=Scientific Image Analysis\nType=Application\nCategories=Education;Science;ImageProcessing;\nExec=/opt/celldetection/start_celldetection.sh\nTryExec==/opt/celldetection/start_celldetection.sh\nTerminal=true\nStartupNotify=true\nMimeType=image/*;\nIcon=/opt/celldetection/napari-icon.ico\nStartupWMClass=celldetection\n' > /home/biop/Desktop/celldetection.desktop \
30+
&& chown -R biop:biop /home/biop \
31+
&& chmod +x /home/biop/Desktop/celldetection.desktop
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33+
34+
RUN chmod -R a+rwX /home/biop/ \
35+
&& chown -R biop:biop /home/biop/
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37+
#################################################################
38+
# Container start
39+
USER biop
40+
WORKDIR /home/biop
41+
ENTRYPOINT ["/usr/local/bin/jupyter"]
42+
CMD ["lab", "--allow-root", "--ip=*", "--port=8888", "--no-browser", "--NotebookApp.token=''", "--NotebookApp.allow_origin='*'", "--notebook-dir=/home/biop"]

‎docker/celldetection/env_celldetection.yml‎

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name: "celldetection"
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channels:
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- pytorch
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- nvidia
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- conda-forge
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- defaults
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dependencies:
8+
- python=3.9
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- pytorch
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- pyqt
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- napari
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- torchvision
13+
- pytorch-cuda=11.8
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- pip
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- pip :
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- celldetection
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- git+https://github.com/FZJ-INM1-BDA/celldetection-napari.git
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- ipykernel
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prefix: "/opt/conda/envs/celldetection"

‎docker/celldetection/start_celldetection.sh‎

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source activate celldetection
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napari
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$ read -rsp $'Press enter to continue...\n'
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Press enter to continue...

‎docker/empanada/Dockerfile-empanada‎

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ARG BASE_IMAGE=0.0.1
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FROM biop-vnc-base:${BASE_IMAGE}
1+
ARG BASE_IMAGE=0.0.3
2+
ARG ALIAS=biop/
3+
FROM ${ALIAS}biop-vnc-base:${BASE_IMAGE} as base
34
#ARG DEBIO_VERSION=0.10.1
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#FROM biop-devbio:${DEBIO_VERSION} as base
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