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various improvements

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chrisfilo committed Sep 1, 2016
1 parent c0aab2f commit 3ab8cc31216dfe9ca46f151d093dea5edadd8cb0
Showing with 18 additions and 14 deletions.
  1. +2 −5 Dockerfile
  2. +15 −9 circle.yml
  3. +1 −0 version
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@@ -10,15 +10,12 @@ RUN apt-get update \
&& apt-get install -y python3-pip python3-matplotlib python3-scipy \
python3-nibabel python3-sklearn
RUN pip3 install nilearn
RUN mkdir -p /code
RUN mkdir /oasis
RUN mkdir /projects
RUN mkdir /scratch
RUN mkdir /local-scratch
COPY run.py /code/run.py
COPY main.py /code/main.py
COPY version /version
ENTRYPOINT ["/code/run.py"]
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@@ -15,23 +15,29 @@ dependencies:
# https://googledrive.com/host/0B2JWN60ZLkgkMEw4bW5VUUpSdFU/ds005-deriv-light.tar
- if [[ ! -d ~/data/ds005-deriv-3subjects/derivatives ]]; then wget -c -P ${HOME}/downloads/ "https://googledrive.com/host/0B2JWN60ZLkgkMEw4bW5VUUpSdFU/ds005-deriv-light.tar" && mkdir -p ${HOME}/data && tar xf ${HOME}/downloads/ds005-deriv-light.tar -C ${HOME}/data; fi
- if [[ -e ~/docker/image.tar ]]; then docker load -i ~/docker/image.tar; fi
- git describe --tags > version
- docker build -t bids/${CIRCLE_PROJECT_REPONAME,,} . :
timeout: 21600
- mkdir -p ~/docker; docker save "bids/${CIRCLE_PROJECT_REPONAME,,}" > ~/docker/image.tar
- mkdir -p ${HOME}/outputs
test:
override:
- docker run -ti --rm -v ${HOME}/data/ds005-deriv-light/derivatives:/bids_dataset -v ${HOME}/outputs:/outputs bids/${CIRCLE_PROJECT_REPONAME,,} /bids_dataset /outputs participant --participant_label 01 :
- docker run -ti --rm --read-only -v /tmp:/tmp -v /var/tmp:/var/tmp -v ${HOME}/data/ds005-deriv-light/derivatives:/bids_dataset -v ${HOME}/outputs:/outputs bids/${CIRCLE_PROJECT_REPONAME,,} /bids_dataset /outputs participant --participant_label 01 :
timeout: 21600
- docker run -ti --rm -v ${HOME}/data/ds005-deriv-light/derivatives:/bids_dataset -v ${HOME}/outputs:/outputs bids/${CIRCLE_PROJECT_REPONAME,,} /bids_dataset /outputs participant --participant_label 02 :
- docker run -ti --rm --read-only -v /tmp:/tmp -v /var/tmp:/var/tmp -v ${HOME}/data/ds005-deriv-light/derivatives:/bids_dataset -v ${HOME}/outputs:/outputs bids/${CIRCLE_PROJECT_REPONAME,,} /bids_dataset /outputs participant --participant_label 02 :
timeout: 21600
- docker run -ti --rm -v ${HOME}/data/ds005-deriv-light/derivatives:/bids_dataset -v ${HOME}/outputs:/outputs bids/${CIRCLE_PROJECT_REPONAME,,} /bids_dataset /outputs participant --participant_label 03 :
- docker run -ti --rm --read-only -v /tmp:/tmp -v /var/tmp:/var/tmp -v ${HOME}/data/ds005-deriv-light/derivatives:/bids_dataset -v ${HOME}/outputs:/outputs bids/${CIRCLE_PROJECT_REPONAME,,} /bids_dataset /outputs participant --participant_label 03 :
timeout: 21600
- docker run -ti --rm -v ${HOME}/data/ds005-deriv-light/derivatives:/bids_dataset -v ${HOME}/outputs:/outputs bids/${CIRCLE_PROJECT_REPONAME,,} /bids_dataset /outputs group :
- docker run -ti --rm --read-only -v /tmp:/tmp -v /var/tmp:/var/tmp -v ${HOME}/data/ds005-deriv-light/derivatives:/bids_dataset -v ${HOME}/outputs:/outputs bids/${CIRCLE_PROJECT_REPONAME,,} /bids_dataset /outputs group :
timeout: 21600
#deployment:
# hub:
# branch: master
# commands:
# - if [[ -n "$DOCKER_PASS" ]]; then docker login -e $DOCKER_EMAIL -u $DOCKER_USER -p $DOCKER_PASS && docker push $DOCKER_REPO; fi
deployment:
hub:
owner: BIDS-Apps
tag: /.*/
commands:
- if [[ -n "$DOCKER_PASS" ]]; then docker login -e $DOCKER_EMAIL -u $DOCKER_USER -p $DOCKER_PASS && docker push bids/${CIRCLE_PROJECT_REPONAME}:latest; fi :
timeout: 21600
- if [[ -n "$DOCKER_PASS" ]]; then docker login -e $DOCKER_EMAIL -u $DOCKER_USER -p $DOCKER_PASS && docker tag bids/${CIRCLE_PROJECT_REPONAME} bids/${CIRCLE_PROJECT_REPONAME}:$CIRCLE_TAG && docker push bids/${CIRCLE_PROJECT_REPONAME}:$CIRCLE_TAG; fi :
timeout: 21600
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@@ -0,0 +1 @@
dev

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