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Dockerfile
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FROM celiib/neurd:v2
LABEL maintainer="Brendan Celli <[email protected]>, Stelios Papadopoulos <[email protected]>"
RUN apt-get update --yes && \
apt-get upgrade --yes && \
apt-get install --yes --no-install-recommends
RUN pip3 install \
nglui \
caveclient
# Install DataJoint with datajoint_plus
ADD "https://api.github.com/repos/cajal/datajoint-plus/releases?per_page=1" latest
RUN pip install datajoint-plus
# Install wridgets
ADD "https://api.github.com/repos/spapa013/wridgets/releases?per_page=1" latest
RUN pip install wridgets
# Install Cajal packages from latest tag
ADD "https://api.github.com/repos/cajal/microns-utils/releases?per_page=1" latest
RUN pip install microns-utils
ADD "https://api.github.com/repos/cajal/microns-nda/releases?per_page=1" latest
RUN export TAG=$(curl -s 'https://api.github.com/repos/cajal/microns-nda/releases?per_page=1' | grep -oP '"name": "\K(.*)(?=")'); \
pip install git+https://github.com/cajal/microns-nda.git@$TAG#subdirectory=python/microns-nda-api
ADD "https://api.github.com/repos/cajal/microns-materialization/releases?per_page=1" latest
RUN export TAG=$(curl -s 'https://api.github.com/repos/cajal/microns-materialization/releases?per_page=1' | grep -oP '"name": "\K(.*)(?=")'); \
pip install git+https://github.com/cajal/microns-materialization.git@$TAG#subdirectory=python/microns-materialization-api
ADD "https://api.github.com/repos/cajal/microns-coregistration/releases?per_page=1" latest
RUN export TAG=$(curl -s 'https://api.github.com/repos/cajal/microns-coregistration/releases?per_page=1' | grep -oP '"name": "\K(.*)(?=")'); \
pip install git+https://github.com/cajal/microns-coregistration.git@$TAG#subdirectory=python/microns-coregistration-api
ADD "https://api.github.com/repos/cajal/microns-manual-proofreading/releases?per_page=1" latest
RUN export TAG=$(curl -s 'https://api.github.com/repos/cajal/microns-manual-proofreading/tags?per_page=1' | grep -oP '"name": "\K(.*)(?=")'); \
pip install git+https://github.com/cajal/microns-manual-proofreading.git@$TAG#subdirectory=python/microns-manual-proofreading-api
ADD "https://api.github.com/repos/cajal/microns-proximities/releases?per_page=1" latest
RUN export TAG=$(curl -s 'https://api.github.com/repos/cajal/microns-proximities/tags?per_page=1' | grep -oP '"name": "\K(.*)(?=")'); \
pip install git+https://github.com/cajal/microns-proximities.git@$TAG#subdirectory=python/microns-proximities-api
# NEURD
ADD "https://api.github.com/repos/reimerlab/neurd/releases?per_page=1" latest
RUN export TAG=$(curl -s 'https://api.github.com/repos/reimerlab/neurd/tags?per_page=1' | grep -oP '"name": "\K(.*)(?=")'); \
pip install git+https://github.com/reimerlab/NEURD.git@$TAG
# install meshAfterParty
WORKDIR /src
ARG GITHUB_TOKEN
RUN [ -n "$GITHUB_TOKEN" ] && git clone https://[email protected]/celiibrendan/meshAfterParty.git || echo "GITHUB_TOKEN is not provided, skipping clone."
RUN pip install git+https://github.com/cajal/minnie-config.git
WORKDIR /
ARG CLOUDVOLUME_TOKEN
RUN mkdir -p .cloudvolume/secrets
RUN echo "{\"token\": \"${CLOUDVOLUME_TOKEN:-}\"}" > .cloudvolume/secrets/cave-secret.json
COPY . /src/microns-morphology
RUN pip install -e /src/microns-morphology/python/microns-morphology
RUN pip install -e /src/microns-morphology/python/microns-morphology-api