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Commit 7002571

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oestebanoesteban
authoredMar 26, 2020
Merge pull request #80 from mgxd/ci/circle
MAINT: Add docker image/circle build
·
24.1.120.0.0rc1
2 parents 838d385 + d550f9f commit 7002571

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‎.circleci/config.yml

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version: 2
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jobs:
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build:
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machine:
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image: circleci/classic:201808-01
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working_directory: /tmp/src/nitransforms
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environment:
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TZ: "/usr/share/zoneinfo/America/Los_Angeles"
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SCRATCH: "/scratch"
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steps:
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- restore_cache:
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keys:
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- build-v1-{{ .Branch }}-{{ epoch }}
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- build-v1-{{ .Branch }}-
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- build-v1-master-
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- build-v1-
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paths:
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- /tmp/docker
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- run:
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name: Set-up a Docker registry
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command: |
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docker run -d -p 5000:5000 --restart=always --name=registry \
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-v /tmp/docker:/var/lib/registry registry:2
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- run:
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name: Pull existing images
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command: |
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set +e
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docker pull localhost:5000/ubuntu
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success=$?
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set -e
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if [[ "$success" = "0" ]]; then
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echo "Pulling from local registry"
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docker tag localhost:5000/ubuntu ubuntu:xenial-20200114
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docker pull localhost:5000/nitransforms
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docker tag localhost:5000/nitransforms nitransforms:latest
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else
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echo "Pulling from Docker Hub"
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docker pull ubuntu:xenial-20200114
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docker tag ubuntu:xenial-20200114 localhost:5000/ubuntu
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docker push localhost:5000/ubuntu
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fi
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- checkout
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- run:
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name: Build Docker image & push to registry
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no_output_timeout: 60m
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command: |
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e=1 && for i in {1..5}; do
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docker build --rm --cache-from=nitransforms:latest \
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-t nitransforms:latest \
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--build-arg BUILD_DATE=`date -u +"%Y-%m-%dT%H:%M:%SZ"` \
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--build-arg VCS_REF=`git rev-parse --short HEAD` . \
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&& e=0 && break || sleep 15
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done && [ "$e" -eq "0" ]
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docker tag nitransforms:latest localhost:5000/nitransforms
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docker push localhost:5000/nitransforms
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- run:
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name: Docker registry garbage collection
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command: |
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docker exec -it registry /bin/registry garbage-collect --delete-untagged \
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/etc/docker/registry/config.yml
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- save_cache:
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key: build-v1-{{ .Branch }}-{{ epoch }}
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paths:
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- /tmp/docker
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- run:
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name: Store FreeSurfer license file
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command: |
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mkdir -p /tmp/fslicense
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cd /tmp/fslicense
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echo "cHJpbnRmICJrcnp5c3p0b2YuZ29yZ29sZXdza2lAZ21haWwuY29tXG41MTcyXG4gKkN2dW12RVYzelRmZ1xuRlM1Si8yYzFhZ2c0RVxuIiA+IGxpY2Vuc2UudHh0Cg==" | base64 -d | sh
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- persist_to_workspace:
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root: /tmp
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paths:
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- fslicense
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test_pytest:
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machine:
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image: circleci/classic:201808-01
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environment:
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FS_LICENSE: "/tmp/fslicense/license.txt"
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working_directory: /tmp/tests
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steps:
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- attach_workspace:
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at: /tmp
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- checkout:
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path: /tmp/src/nitransforms
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- run:
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name: Get codecov
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command: python -m pip install codecov
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- restore_cache:
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keys:
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- build-v1-{{ .Branch }}-{{ epoch }}
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- build-v1-{{ .Branch }}-
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- build-v1-master-
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- build-v1-
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- run:
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name: Set-up a Docker registry & pull
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command: |
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docker run -d -p 5000:5000 --restart=always --name=registry \
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-v /tmp/docker:/var/lib/registry registry:2
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docker pull localhost:5000/nitransforms
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docker tag localhost:5000/nitransforms nitransforms:latest
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- run:
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name: Run unit tests
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no_output_timeout: 2h
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command: |
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mkdir -p $PWD/artifacts $PWD/summaries
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sudo setfacl -d -m group:ubuntu:rwx $PWD
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sudo setfacl -m group:ubuntu:rwx $PWD
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docker run -u $( id -u ) -it --rm=false -w /src/nitransforms \
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-e COVERAGE_FILE=/tmp/summaries/.pytest.coverage \
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-v /tmp/fslicense/license.txt:/opt/freesurfer/license.txt:ro \
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-v ${PWD}:/tmp nitransforms:latest \
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pytest --junit-xml=/tmp/summaries/pytest.xml \
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--cov nitransforms --cov-report xml:/tmp/summaries/unittests.xml \
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nitransforms/
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- run:
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name: Submit unit test coverage
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command: |
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cd /tmp/src/nitransforms
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python -m codecov --file /tmp/tests/summaries/unittests.xml \
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--flags unittests -e CIRCLE_JOB
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- run:
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name: Clean up tests directory
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when: on_success
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command: |
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rm -rf /tmp/tests/pytest-of-root
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- store_artifacts:
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path: /tmp/tests/artifacts
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- store_test_results:
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path: /tmp/tests/summaries/
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test_packaging_and_deploy:
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machine:
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image: circleci/classic:201808-01
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working_directory: /tmp/src/nitransforms
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steps:
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- checkout
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- run: pyenv local 3.7.0
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- run:
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name: Install build depends
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command: python3 -m pip install "setuptools>=30.4.0" "pip>=10.0.1" "twine<2.0" docutils
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- run:
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name: Build and check
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command: |
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python3 setup.py check -r -s
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python3 setup.py sdist
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python3 -m twine check dist/*
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- run:
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name: Validate version
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command: |
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THISVERSION=$( python3 get_version.py )
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python3 -m pip install dist/*.tar.gz
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mkdir empty
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cd empty
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INSTALLED=$( python3 -c 'import nitransforms; print(nitransforms.__version__)' )
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test "${CIRCLE_TAG:-$THISVERSION}" == "$INSTALLED"
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- run:
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name: Upload to PyPi
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command: |
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python3 -m twine upload dist/*
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workflows:
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version: 2
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build_test_deploy:
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jobs:
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- build:
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filters:
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branches:
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ignore:
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- /docs?\/.*/
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tags:
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only: /.*/
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- test_pytest:
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requires:
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- build
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filters:
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branches:
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ignore:
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- /docs?\/.*/
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- /docker\/.*/
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tags:
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only: /.*/
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- test_packaging_and_deploy:
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requires:
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- test_pytest
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filters:
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branches:
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ignore: /.*/
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tags:
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only: /.*/

‎Dockerfile

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FROM ubuntu:xenial-20200114
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# Pre-cache neurodebian key
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COPY docker/files/neurodebian.gpg /usr/local/etc/neurodebian.gpg
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# Prepare environment
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RUN apt-get update && \
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apt-get install -y --no-install-recommends \
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curl \
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bzip2 \
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ca-certificates \
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xvfb \
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build-essential \
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autoconf \
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libtool \
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pkg-config \
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git && \
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curl -sL https://deb.nodesource.com/setup_10.x | bash - && \
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apt-get install -y --no-install-recommends \
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nodejs && \
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apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
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# Installing freesurfer
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RUN curl -sSL https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.1/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1.tar.gz | tar zxv --no-same-owner -C /opt \
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--exclude='freesurfer/diffusion' \
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--exclude='freesurfer/docs' \
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--exclude='freesurfer/fsfast' \
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--exclude='freesurfer/lib/cuda' \
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--exclude='freesurfer/lib/qt' \
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--exclude='freesurfer/matlab' \
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--exclude='freesurfer/mni/share/man' \
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--exclude='freesurfer/subjects/fsaverage_sym' \
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--exclude='freesurfer/subjects/fsaverage3' \
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--exclude='freesurfer/subjects/fsaverage4' \
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--exclude='freesurfer/subjects/cvs_avg35' \
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--exclude='freesurfer/subjects/cvs_avg35_inMNI152' \
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--exclude='freesurfer/subjects/bert' \
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--exclude='freesurfer/subjects/lh.EC_average' \
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--exclude='freesurfer/subjects/rh.EC_average' \
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--exclude='freesurfer/subjects/sample-*.mgz' \
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--exclude='freesurfer/subjects/V1_average' \
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--exclude='freesurfer/trctrain'
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ENV FSL_DIR="/usr/share/fsl/5.0" \
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OS="Linux" \
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FS_OVERRIDE=0 \
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FIX_VERTEX_AREA="" \
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FSF_OUTPUT_FORMAT="nii.gz" \
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FREESURFER_HOME="/opt/freesurfer"
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ENV SUBJECTS_DIR="$FREESURFER_HOME/subjects" \
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FUNCTIONALS_DIR="$FREESURFER_HOME/sessions" \
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MNI_DIR="$FREESURFER_HOME/mni" \
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LOCAL_DIR="$FREESURFER_HOME/local" \
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MINC_BIN_DIR="$FREESURFER_HOME/mni/bin" \
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MINC_LIB_DIR="$FREESURFER_HOME/mni/lib" \
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MNI_DATAPATH="$FREESURFER_HOME/mni/data"
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ENV PERL5LIB="$MINC_LIB_DIR/perl5/5.8.5" \
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MNI_PERL5LIB="$MINC_LIB_DIR/perl5/5.8.5" \
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PATH="$FREESURFER_HOME/bin:$FSFAST_HOME/bin:$FREESURFER_HOME/tktools:$MINC_BIN_DIR:$PATH"
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# Installing Neurodebian packages (FSL, AFNI, git)
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RUN curl -sSL "http://neuro.debian.net/lists/$( lsb_release -c | cut -f2 ).us-ca.full" >> /etc/apt/sources.list.d/neurodebian.sources.list && \
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apt-key add /usr/local/etc/neurodebian.gpg && \
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(apt-key adv --refresh-keys --keyserver hkp://ha.pool.sks-keyservers.net 0xA5D32F012649A5A9 || true)
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RUN apt-get update && \
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apt-get install -y --no-install-recommends \
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fsl-core=5.0.9-5~nd16.04+1 \
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fsl-mni152-templates=5.0.7-2 \
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afni=16.2.07~dfsg.1-5~nd16.04+1 \
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convert3d \
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connectome-workbench=1.3.2-2~nd16.04+1 \
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git-annex-standalone && \
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apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
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ENV FSLDIR="/usr/share/fsl/5.0" \
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FSLOUTPUTTYPE="NIFTI_GZ" \
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FSLMULTIFILEQUIT="TRUE" \
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POSSUMDIR="/usr/share/fsl/5.0" \
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LD_LIBRARY_PATH="/usr/lib/fsl/5.0:$LD_LIBRARY_PATH" \
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FSLTCLSH="/usr/bin/tclsh" \
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FSLWISH="/usr/bin/wish" \
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AFNI_MODELPATH="/usr/lib/afni/models" \
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AFNI_IMSAVE_WARNINGS="NO" \
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AFNI_TTATLAS_DATASET="/usr/share/afni/atlases" \
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AFNI_PLUGINPATH="/usr/lib/afni/plugins"
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ENV PATH="/usr/lib/fsl/5.0:/usr/lib/afni/bin:$PATH"
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# Installing ANTs 2.2.0 (NeuroDocker build)
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ENV ANTSPATH=/usr/lib/ants
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RUN mkdir -p $ANTSPATH && \
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curl -sSL "https://dl.dropbox.com/s/2f4sui1z6lcgyek/ANTs-Linux-centos5_x86_64-v2.2.0-0740f91.tar.gz" \
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| tar -xzC $ANTSPATH --strip-components 1
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ENV PATH=$ANTSPATH:$PATH
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# Installing and setting up miniconda
97+
RUN curl -sSLO https://repo.continuum.io/miniconda/Miniconda3-4.5.11-Linux-x86_64.sh && \
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bash Miniconda3-4.5.11-Linux-x86_64.sh -b -p /usr/local/miniconda && \
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rm Miniconda3-4.5.11-Linux-x86_64.sh
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# Set CPATH for packages relying on compiled libs (e.g. indexed_gzip)
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ENV PATH="/usr/local/miniconda/bin:$PATH" \
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CPATH="/usr/local/miniconda/include/:$CPATH" \
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LANG="C.UTF-8" \
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LC_ALL="C.UTF-8" \
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PYTHONNOUSERSITE=1
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# Installing precomputed python packages
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RUN conda install -y python=3.7.1 \
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pip=19.1 \
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mkl=2018.0.3 \
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mkl-service \
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numpy=1.15.4 \
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scipy=1.1.0 \
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libxml2=2.9.8 \
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libxslt=1.1.32 \
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zlib; sync && \
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chmod -R a+rX /usr/local/miniconda; sync && \
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chmod +x /usr/local/miniconda/bin/*; sync && \
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conda build purge-all; sync && \
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conda clean -tipsy && sync
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# Unless otherwise specified each process should only use one thread - nipype
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# will handle parallelization
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ENV MKL_NUM_THREADS=1 \
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OMP_NUM_THREADS=1
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# Create a shared $HOME directory
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RUN useradd -m -s /bin/bash -G users neuro
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WORKDIR /home/neuro
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ENV HOME="/home/neuro"
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# Install package
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COPY . /src/nitransforms
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ARG VERSION
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# Force static versioning within container
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RUN echo "${VERSION}" > /src/nitransforms/nitransforms/VERSION && \
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echo "include nitransforms/VERSION" >> /src/nitransforms/MANIFEST.in && \
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pip install --no-cache-dir "/src/nitransforms[all]"
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RUN find $HOME -type d -exec chmod go=u {} + && \
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find $HOME -type f -exec chmod go=u {} +
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144+
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RUN ldconfig
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WORKDIR /tmp/
147+
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ARG BUILD_DATE
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ARG VCS_REF
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ARG VERSION
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LABEL org.label-schema.build-date=$BUILD_DATE \
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org.label-schema.name="nitransforms" \
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org.label-schema.vcs-url="https://github.com/poldracklab/nitransforms" \
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org.label-schema.version=$VERSION \
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org.label-schema.schema-version="1.0"

‎docker/files/neurodebian.gpg

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-----BEGIN PGP PUBLIC KEY BLOCK-----
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Version: GnuPG v1
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