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chrisgorgo committed Oct 25, 2017
1 parent eea3695 commit 4c9239d
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13 changes: 6 additions & 7 deletions circle.yml
Original file line number Diff line number Diff line change
Expand Up @@ -22,21 +22,20 @@ dependencies:
- docker build -t bids/${CIRCLE_PROJECT_REPONAME} . :
timeout: 21600
- mkdir -p ~/docker; docker save "bids/${CIRCLE_PROJECT_REPONAME}" > ~/docker/image.tar
- mkdir -p /opt/freesurfer && echo "cHJpbnRmICJrcnp5c3p0b2YuZ29yZ29sZXdza2lAZ21haWwuY29tXG41MTcyXG4gKkN2dW12RVYzelRmZ1xuRlM1Si8yYzFhZ2c0RVxuIiA+IC9vcHQvZnJlZXN1cmZlci9saWNlbnNlLnR4dAo=" | base64 -d | sh
- cp license.txt /tmp/
- echo "cHJpbnRmICJrcnp5c3p0b2YuZ29yZ29sZXdza2lAZ21haWwuY29tXG41MTcyXG4gKkN2dW12RVYzelRmZ1xuRlM1Si8yYzFhZ2c0RVxuIiA+IGxpY2Vuc2UudHh0Cg==" | base64 -d | sh

test:
override:
# print version
- docker run -ti --rm --read-only -v /tmp:/tmp -v /var/tmp:/var/tmp -v ${HOME}/data/ds114_test1:/bids_dataset bids/${CIRCLE_PROJECT_REPONAME,,} --version
- docker run -ti --rm --read-only -v /tmp:/tmp -v /var/tmp:/var/tmp -v ${HOME}/data/ds114_test1:/bids_dataset -v ${HOME}/outputs1:/outputs bids/${CIRCLE_PROJECT_REPONAME,,} /bids_dataset /outputs participant --participant_label 01 --license_file=/opt/freesurfer/license.txt --stages autorecon1 && cat ${HOME}/outputs1/sub-01/scripts/recon-all.done :
- docker run -ti --rm --read-only -v $PWD/license.txt:/license.txt -v /tmp:/tmp -v /var/tmp:/var/tmp -v ${HOME}/data/ds114_test1:/bids_dataset bids/${CIRCLE_PROJECT_REPONAME,,} --version
- docker run -ti --rm --read-only -v $PWD/license.txt:/license.txt -v /tmp:/tmp -v /var/tmp:/var/tmp -v ${HOME}/data/ds114_test1:/bids_dataset -v ${HOME}/outputs1:/outputs bids/${CIRCLE_PROJECT_REPONAME,,} /bids_dataset /outputs participant --participant_label 01 --license_file=/license.txt --stages autorecon1 && cat ${HOME}/outputs1/sub-01/scripts/recon-all.done :
timeout: 21600
- docker run -ti --rm --read-only -v /tmp:/tmp -v /var/tmp:/var/tmp -v ${HOME}/data/ds114_test2:/bids_dataset -v ${HOME}/outputs2:/outputs bids/${CIRCLE_PROJECT_REPONAME,,} /bids_dataset /outputs participant --participant_label 01 --steps cross-sectional --session_label test --license_file=/opt/freesurfer/license.txt --stages autorecon1 && cat ${HOME}/outputs2/sub-01_ses-test/scripts/recon-all.done :
- docker run -ti --rm --read-only -v $PWD/license.txt:/license.txt -v /tmp:/tmp -v /var/tmp:/var/tmp -v ${HOME}/data/ds114_test2:/bids_dataset -v ${HOME}/outputs2:/outputs bids/${CIRCLE_PROJECT_REPONAME,,} /bids_dataset /outputs participant --participant_label 01 --steps cross-sectional --session_label test --license_file=/license.txt --stages autorecon1 && cat ${HOME}/outputs2/sub-01_ses-test/scripts/recon-all.done :
timeout: 21600
# group2 tests
- docker run -ti --rm --read-only -v /tmp:/tmp -v /var/tmp:/var/tmp -v ${HOME}/data/ds114_test1:/bids_dataset -v ${HOME}/data/ds114_test1_freesurfer_precomp_v6.0.0:/outputs bids/${CIRCLE_PROJECT_REPONAME,,} /bids_dataset /outputs group2 --license_file=/opt/freesurfer/license.txt && mkdir -p ${HOME}/outputs1/ && sudo mv ${HOME}/data/ds114_test1_freesurfer_precomp_v6.0.0/00_group* ${HOME}/outputs1/ && cat ${HOME}/outputs1/00_group2_stats_tables/lh.aparc.thickness.tsv :
- docker run -ti --rm --read-only -v $PWD/license.txt:/license.txt -v /tmp:/tmp -v /var/tmp:/var/tmp -v ${HOME}/data/ds114_test1:/bids_dataset -v ${HOME}/data/ds114_test1_freesurfer_precomp_v6.0.0:/outputs bids/${CIRCLE_PROJECT_REPONAME,,} /bids_dataset /outputs group2 --license_file=/license.txt && mkdir -p ${HOME}/outputs1/ && sudo mv ${HOME}/data/ds114_test1_freesurfer_precomp_v6.0.0/00_group* ${HOME}/outputs1/ && cat ${HOME}/outputs1/00_group2_stats_tables/lh.aparc.thickness.tsv :
timeout: 21600
- docker run -ti --rm --read-only -v /tmp:/tmp -v /var/tmp:/var/tmp -v ${HOME}/data/ds114_test2:/bids_dataset -v ${HOME}/data/ds114_test2_freesurfer_precomp_v6.0.0:/outputs bids/${CIRCLE_PROJECT_REPONAME,,} /bids_dataset /outputs group2 --license_file=/opt/freesurfer/license.txt && mkdir -p ${HOME}/outputs2/ && sudo mv ${HOME}/data/ds114_test2_freesurfer_precomp_v6.0.0/00_group* ${HOME}/outputs2/ && cat ${HOME}/outputs2/00_group2_stats_tables/lh.aparc.thickness.tsv :
- docker run -ti --rm --read-only -v $PWD/license.txt:/license.txt -v /tmp:/tmp -v /var/tmp:/var/tmp -v ${HOME}/data/ds114_test2:/bids_dataset -v ${HOME}/data/ds114_test2_freesurfer_precomp_v6.0.0:/outputs bids/${CIRCLE_PROJECT_REPONAME,,} /bids_dataset /outputs group2 --license_file=/license.txt && mkdir -p ${HOME}/outputs2/ && sudo mv ${HOME}/data/ds114_test2_freesurfer_precomp_v6.0.0/00_group* ${HOME}/outputs2/ && cat ${HOME}/outputs2/00_group2_stats_tables/lh.aparc.thickness.tsv :
timeout: 21600

deployment:
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4 changes: 0 additions & 4 deletions license.txt

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