fix permissions in circleci

Author: oesteban

circle.yml

@@ -7,6 +7,7 @@ machine:
     DATA_NIPYPE_TUTORIAL_URL: "${OSF_NIPYPE_URL}/57f4739cb83f6901ed94bf21"
     DATA_NIPYPE_FSL_COURSE: "${OSF_NIPYPE_URL}/57f472cf9ad5a101f977ecfe"
     DATA_NIPYPE_FSL_FEEDS: "${OSF_NIPYPE_URL}/57f473066c613b01f113e7af"
+    SCRATCH: "$HOME/scratch"
   services:
     - docker
 
@@ -20,9 +21,10 @@ dependencies:
     # Let CircleCI cache the apt archive
     - mkdir -p ~/.apt-cache/partial && sudo rm -rf /var/cache/apt/archives && sudo ln -s ~/.apt-cache /var/cache/apt/archives
     - sudo apt-get -y update && sudo apt-get install -y wget bzip2
-
+    # Create scratch folder and force group permissions
+    - mkdir -p $SCRATCH && sudo setfacl -d -m group:ubuntu:rwx $SCRATCH && sudo setfacl -m group:ubuntu:rwx $SCRATCH
+    - mkdir -p $HOME/docker $HOME/examples $SCRATCH/pytest $SCRATCH
   override:
-    - mkdir -p $HOME/docker $HOME/examples $HOME/scratch/pytest $HOME/scratch/logs
     - if [[ ! -d ~/examples/nipype-tutorial ]]; then wget --retry-connrefused --waitretry=5 --read-timeout=20 --timeout=15 -t 0 -q -O nipype-tutorial.tar.bz2 "${DATA_NIPYPE_TUTORIAL_URL}" && tar xjf nipype-tutorial.tar.bz2 -C ~/examples/; fi
     - if [[ ! -d ~/examples/nipype-fsl_course_data ]]; then wget --retry-connrefused --waitretry=5 --read-timeout=20 --timeout=15 -t 0 -q -O nipype-fsl_course_data.tar.gz "${DATA_NIPYPE_FSL_COURSE}" && tar xzf nipype-fsl_course_data.tar.gz -C ~/examples/; fi
     - if [[ ! -d ~/examples/feeds ]]; then wget --retry-connrefused --waitretry=5 --read-timeout=20 --timeout=15 -t 0 -q -O fsl-5.0.9-feeds.tar.gz "${DATA_NIPYPE_FSL_FEEDS}" && tar xzf fsl-5.0.9-feeds.tar.gz -C ~/examples/; fi

docker/files/tests.sh

@@ -14,24 +14,24 @@ fi
 # They may need to be rebalanced in the future.
 case ${CIRCLE_NODE_INDEX} in
   0)
-    time docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_spm_dartel Linear /root/examples/ level1
+    time docker run -v /etc/localtime:/etc/localtime:ro -v $HOME/examples:/root/examples:ro -v $SCRATCH:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_spm_dartel Linear /root/examples/ level1
     ;;
   1)
-    time docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_spm_dartel Linear /root/examples/ l2pipeline
-    time docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh test_spm Linear /root/examples/ workflow3d
-    time docker run -v /etc/localtime:/etc/localtime:ro -e FSL_COURSE_DATA="/root/examples/nipype-fsl_course_data" -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /root/src/nipype nipype/nipype_test:py35 /usr/bin/run_pytests.sh py35
-    time docker run -v /etc/localtime:/etc/localtime:ro -e NIPYPE_NUMBER_OF_CPUS=4 -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py27 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /root/examples/ level1
+    time docker run -v /etc/localtime:/etc/localtime:ro -v $HOME/examples:/root/examples:ro -v $SCRATCH:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_spm_dartel Linear /root/examples/ l2pipeline
+    time docker run -v /etc/localtime:/etc/localtime:ro -v $HOME/examples:/root/examples:ro -v $SCRATCH:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh test_spm Linear /root/examples/ workflow3d
+    time docker run -v /etc/localtime:/etc/localtime:ro -e FSL_COURSE_DATA="/root/examples/nipype-fsl_course_data" -v $HOME/examples:/root/examples:ro -v $SCRATCH:/scratch -w /root/src/nipype nipype/nipype_test:py35 /usr/bin/run_pytests.sh py35
+    time docker run -v /etc/localtime:/etc/localtime:ro -e NIPYPE_NUMBER_OF_CPUS=4 -v $HOME/examples:/root/examples:ro -v $SCRATCH:/scratch -w /scratch nipype/nipype_test:py27 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /root/examples/ level1
     ;;
   2)
-    time docker run -v /etc/localtime:/etc/localtime:ro -e NIPYPE_NUMBER_OF_CPUS=4 -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /root/examples/ l2pipeline
-    time docker run -v /etc/localtime:/etc/localtime:ro -v ~/scratch:/scratch -w /root/src/nipype/doc nipype/nipype_test:py35 /usr/bin/run_builddocs.sh
-    time docker run -v /etc/localtime:/etc/localtime:ro -e FSL_COURSE_DATA="/root/examples/nipype-fsl_course_data" -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /root/src/nipype nipype/nipype_test:py27 /usr/bin/run_pytests.sh py27
-    time docker run -v /etc/localtime:/etc/localtime:ro -e NIPYPE_NUMBER_OF_CPUS=4 -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /root/examples/ level1
+    time docker run -v /etc/localtime:/etc/localtime:ro -e NIPYPE_NUMBER_OF_CPUS=4 -v $HOME/examples:/root/examples:ro -v $SCRATCH:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /root/examples/ l2pipeline
+    time docker run -v /etc/localtime:/etc/localtime:ro -v $SCRATCH:/scratch -w /root/src/nipype/doc nipype/nipype_test:py35 /usr/bin/run_builddocs.sh
+    time docker run -v /etc/localtime:/etc/localtime:ro -e FSL_COURSE_DATA="/root/examples/nipype-fsl_course_data" -v $HOME/examples:/root/examples:ro -v $SCRATCH:/scratch -w /root/src/nipype nipype/nipype_test:py27 /usr/bin/run_pytests.sh py27
+    time docker run -v /etc/localtime:/etc/localtime:ro -e NIPYPE_NUMBER_OF_CPUS=4 -v $HOME/examples:/root/examples:ro -v $SCRATCH:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /root/examples/ level1
     ;;
   3)
-    time docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh test_spm Linear /root/examples/ workflow4d
-    time docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_fsl_feeds Linear /root/examples/ l1pipeline
-    time docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_fsl_reuse Linear /root/examples/ level1_workflow
+    time docker run -v /etc/localtime:/etc/localtime:ro -v $HOME/examples:/root/examples:ro -v $SCRATCH:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh test_spm Linear /root/examples/ workflow4d
+    time docker run -v /etc/localtime:/etc/localtime:ro -v $HOME/examples:/root/examples:ro -v $SCRATCH:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_fsl_feeds Linear /root/examples/ l1pipeline
+    time docker run -v /etc/localtime:/etc/localtime:ro -v $HOME/examples:/root/examples:ro -v $SCRATCH:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_fsl_reuse Linear /root/examples/ level1_workflow
     ;;
 esac