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Merge pull request #15 from BIDS-Apps/circleci2
Circleci2
2 parents 50d4bba + a3cf50f commit 84e3c72

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‎.circleci/config.yml‎

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version: 2
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jobs:
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get_data:
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machine:
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image: circleci/classic:201711-01
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working_directory: /tmp/data
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steps:
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- restore_cache:
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keys:
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- data-v3-{{ .Revision }}
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- data-v3-
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- run:
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name: Get ds114_test1
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command: |
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mkdir -p /tmp/data
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if [[ ! -d /tmp/data/ds114_test1 ]]; then
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wget -c -O ~/ds114_test1.tar \
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"https://files.osf.io/v1/resources/9q7dv/providers/osfstorage/57e54a326c613b01d7d3ed90" && \
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tar xf ~/ds114_test1.tar -C /tmp/data && \
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rm ~/ds114_test1.tar;
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else
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echo "ds114_test1 was cached"
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fi
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- run:
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name: Get ds114_test2
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command: |
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mkdir -p /tmp/data
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if [[ ! -d /tmp/data/ds114_test2 ]]; then
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wget -c -O ~/ds114_test2.tar \
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"https://files.osf.io/v1/resources/9q7dv/providers/osfstorage/57e549f9b83f6901d457d162" && \
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tar xf ~/ds114_test2.tar -C /tmp/data && \
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rm ~/ds114_test2.tar;
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else
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echo "ds114_test2 was cached"
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fi
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- run:
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name: Get ds114_test1_freesurfer
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command: |
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mkdir -p /tmp/data
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if [[ ! -d /tmp/data/ds114_test1_freesurfer ]]; then
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wget -c -O ~/ds114_test1_freesurfer.tar \
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"https://files.osf.io/v1/resources/9q7dv/providers/osfstorage/5882adf3b83f6901f564da49" && \
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tar xf ~/ds114_test1_freesurfer.tar -C /tmp/data && \
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rm ~/ds114_test1_freesurfer.tar;
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else
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echo "ds114_test1_freesurfer was cached"
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fi
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- run:
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name: Get ds114_test2_freesurfer
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command: |
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mkdir -p /tmp/data
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if [[ ! -d /tmp/data/ds114_test2_freesurfer ]]; then
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wget -c -O ~/ds114_test2_freesurfer.tar \
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"https://files.osf.io/v1/resources/9q7dv/providers/osfstorage/5882b0e3b83f6901fb64da18" && \
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tar xf ~/ds114_test2_freesurfer.tar -C /tmp/data && \
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rm ~/ds114_test2_freesurfer.tar;
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else
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echo "ds114_test2_freesurfer was cached"
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fi
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- save_cache:
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key: data-v3-{{ .Revision }}-{{ epoch }}
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paths:
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- /tmp/data
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build:
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docker:
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- image: docker:18.01.0-ce-git
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steps:
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- checkout
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- run:
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name: Install parallel gzip
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command: |
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apk add --no-cache pigz
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- restore_cache:
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keys:
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- docker-v2-{{ .Branch }}-{{ .Revision }}
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- docker-v2-{{ .Branch }}-
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- docker-v2-master-
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- docker-v2-
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paths:
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- /tmp/cache/docker.tar.gz
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- setup_remote_docker
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- run:
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name: Load Docker image layer cache
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no_output_timeout: 30m
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command: |
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docker info
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set +o pipefail
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if [ -f /tmp/cache/docker.tar.gz ]; then
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pigz -d --stdout /tmp/cache/docker.tar.gz | docker load
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else
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echo "No docker cache found"
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fi
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docker images
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- run:
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name: get version
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command: |
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git describe --tags --always > version
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cat version
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- run:
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name: Build Docker image
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no_output_timeout: 60m
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command: |
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docker images
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set +o pipefail
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docker build --cache-from=bids/${CIRCLE_PROJECT_REPONAME} \
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-t bids/${CIRCLE_PROJECT_REPONAME}:latest .
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docker images
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- run:
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name: Docker save
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no_output_timeout: 40m
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command: |
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mkdir -p /tmp/cache
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set +o pipefail
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docker save bids/${CIRCLE_PROJECT_REPONAME}:latest \
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| pigz -2 -p 3 > /tmp/cache/docker.tar.gz
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- save_cache:
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key: docker-v2-{{ .Branch }}-{{ epoch }}
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paths:
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- /tmp/cache/docker.tar.gz
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# Usage and version
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- run:
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name: Usage BIDS
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command: docker run -ti --rm bids/${CIRCLE_PROJECT_REPONAME}:latest -h
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- run:
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name: Usage files
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command: docker run --rm -ti --entrypoint=run_brain_age_files.py bids/${CIRCLE_PROJECT_REPONAME}:latest -h
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- run:
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name: Version BIDS
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command: docker run -ti --rm bids/${CIRCLE_PROJECT_REPONAME}:latest -v
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- run:
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name: Version files
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command: docker run --rm -ti --entrypoint=run_brain_age_files.py bids/${CIRCLE_PROJECT_REPONAME}:latest -v
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- run:
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name: Python packages
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command: docker run --rm -ti --entrypoint=/bin/bash bids/${CIRCLE_PROJECT_REPONAME}:latest -c "pip freeze"
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test:
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machine:
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image: circleci/classic:201711-01
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working_directory: /tmp/data
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environment:
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- DATADIR: '/tmp/data'
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- OUTDIR: '/tmp/outputs'
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steps:
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- run:
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name: Install parallel gzip
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command: |
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sudo apt-get update && sudo apt-get install -y pigz
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- restore_cache:
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keys:
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- docker-v2-{{ .Branch }}-{{ .Revision }}
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- docker-v2-{{ .Branch }}-
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- docker-v2-master-
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- docker-v2-
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paths:
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- /tmp/cache/docker.tar.gz
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- restore_cache:
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keys:
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- data-v3-{{ .Revision }}
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- data-v3-
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# Load Docker
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- run:
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name: Load Docker
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no_output_timeout: 30m
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command: |
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docker info
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set +o pipefail
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pigz -d --stdout /tmp/cache/docker.tar.gz | docker load
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docker images
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- run:
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name: make output directory
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command: mkdir -p ${OUTDIR}
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# Test 1: ds114_test1
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- run:
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name: Test 1 ds114_test1 - 1
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command: |
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docker run --rm -ti -v ${DATADIR}/ds114_test1:/data/in \
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-v ${DATADIR}/ds114_test1_freesurfer:/data/fs \
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-v ${OUTDIR}/ds114_test1:/data/out \
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bids/${CIRCLE_PROJECT_REPONAME}:latest \
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/data/in /data/out participant --freesurfer_dir /data/fs \
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--license_key="~/test.key"
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- run:
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name: Test 1 ds114_test1 - 2
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command: |
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docker run --rm -ti -v ${DATADIR}/ds114_test1:/data/in \
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-v ${DATADIR}/ds114_test1_freesurfer:/data/fs \
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-v ${OUTDIR}/ds114_test1:/data/out \
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bids/${CIRCLE_PROJECT_REPONAME}:latest \
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/data/in /data/out group --freesurfer_dir /data/fs \
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--license_key="~/test.key"
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- run:
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name: Test 1 ds114_test1 - 3
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command: |
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cat ${OUTDIR}/ds114_test1/baracus/00_group/group_predicted_age.tsv
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# Test2 : models
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- run:
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name: Test 2 models - 1
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command: |
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docker run --rm -ti -v ${DATADIR}/ds114_test1:/data/in \
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-v ${DATADIR}/ds114_test1_freesurfer:/data/fs \
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-v ${OUTDIR}/ds114_test1_models:/data/out \
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bids/${CIRCLE_PROJECT_REPONAME}:latest \
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/data/in /data/out participant --freesurfer_dir /data/fs \
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--license_key="~/test.key" \
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--models Liem2016__OCI_norm Liem2016__full_2samp_training
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- run:
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name: Test 2 models - 2
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command: |
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docker run --rm -ti -v ${DATADIR}/ds114_test1:/data/in \
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-v ${DATADIR}/ds114_test1_freesurfer:/data/fs \
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-v ${OUTDIR}/ds114_test1_models:/data/out \
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bids/${CIRCLE_PROJECT_REPONAME}:latest \
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/data/in /data/out group --freesurfer_dir /data/fs \
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--license_key="~/test.key"
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- run:
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name: Test 2 models - 3
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command: |
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cat ${OUTDIR}/ds114_test1_models/baracus/00_group/group_predicted_age.tsv
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# Test3: file mode
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- run:
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name: Test 3 file mode - 1
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command: |
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docker run --rm -ti \
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-v ${OUTDIR}/ds114_test1/baracus/sub-01/data/:/data/in \
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-v ${OUTDIR}/ds114_test1_file_mode:/data/out \
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--entrypoint=run_brain_age_files.py \
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bids/${CIRCLE_PROJECT_REPONAME}:latest \
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/data/out \
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--lh_thickness_file /data/in/lh.thickness.mgh \
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--rh_thickness_file /data/in/rh.thickness.mgh \
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--lh_area_file /data/in/lh.area.mgh \
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--rh_area_file /data/in/rh.area.mgh \
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--aseg_file /data/in/aseg --participant_label sub-01
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- run:
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name: Test 3 file mode - 2
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command: |
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cat ${OUTDIR}/ds114_test1_file_mode/sub-01/sub-01_predicted_age.tsv
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# Test 4: ds114_test2
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- run:
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name: Test 1 ds114_test2 - 1
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command: |
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docker run --rm -ti -v ${DATADIR}/ds114_test2:/data/in \
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-v ${DATADIR}/ds114_test2_freesurfer:/data/fs \
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-v ${OUTDIR}/ds114_test2:/data/out \
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bids/${CIRCLE_PROJECT_REPONAME}:latest \
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/data/in /data/out participant --freesurfer_dir /data/fs \
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--license_key="~/test.key"
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- run:
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name: Test 1 ds114_test2 - 2
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command: |
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docker run --rm -ti -v ${DATADIR}/ds114_test2:/data/in \
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-v ${DATADIR}/ds114_test2_freesurfer:/data/fs \
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-v ${OUTDIR}/ds114_test2:/data/out \
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bids/${CIRCLE_PROJECT_REPONAME}:latest \
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/data/in /data/out group --freesurfer_dir /data/fs \
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--license_key="~/test.key"
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- run:
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name: Test 1 ds114_test2 - 3
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command: |
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cat ${OUTDIR}/ds114_test2/baracus/00_group/group_predicted_age.tsv
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- store_artifacts:
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path: /tmp/outputs/
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deploy:
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machine:
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image: circleci/classic:201711-01
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steps:
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- run:
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name: Install parallel gzip
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command: |
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sudo apt-get update && sudo apt-get install -y pigz
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- restore_cache:
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keys:
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- docker-v2-{{ .Branch }}-{{ .Revision }}
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- docker-v2-{{ .Branch }}-
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- docker-v2-master-
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- docker-v2-
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paths:
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- /tmp/cache/docker.tar.gz
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# Load Docker
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- run:
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name: Load Docker
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no_output_timeout: 30m
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command: |
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docker info
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set +o pipefail
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pigz -d --stdout /tmp/cache/docker.tar.gz | docker load
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docker images
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- run:
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name: Deploy to Docker Hub
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no_output_timeout: 40m
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command: |
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if [[ -n "$DOCKER_PASS" ]]; then
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docker login -u $DOCKER_USER -p $DOCKER_PASS
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docker tag bids/${CIRCLE_PROJECT_REPONAME} bids/${CIRCLE_PROJECT_REPONAME}:unstable
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docker push bids/${CIRCLE_PROJECT_REPONAME}:unstable
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if [[ -n "$CIRCLE_TAG" ]]; then
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docker push bids/${CIRCLE_PROJECT_REPONAME}:latest
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docker tag bids/${CIRCLE_PROJECT_REPONAME} bids/${CIRCLE_PROJECT_REPONAME}:$CIRCLE_TAG
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docker push bids/${CIRCLE_PROJECT_REPONAME}:$CIRCLE_TAG
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fi
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fi
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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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- get_data:
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filters:
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tags:
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only: /.*/
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- build:
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filters:
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tags:
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only: /.*/
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- test:
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requires:
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- get_data
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- build
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filters:
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tags:
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only: /.*/
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- deploy:
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requires:
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- test
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filters:
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branches:
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only: master
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tags:
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only: /.*/

‎Dockerfile‎

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@@ -77,10 +77,10 @@ ENV LANG=C.UTF-8
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ENV LC_ALL=C.UTF-8
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RUN pip install nibabel
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RUN pip install pybids
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RUN pip install duecredit
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RUN pip install nibabel==2.2.0
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RUN pip install pybids==0.3 grabbit==0.0.8
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RUN pip install duecredit==0.6.3
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RUN pip install scikit-learn==0.17.1
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COPY . /code/
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RUN cd /code && ls && pip install -e .

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