{"action":"created","issue":{"url":"https://api.github.com/repos/kaczmarj/neurodocker/issues/219","repository_url":"https://api.github.com/repos/kaczmarj/neurodocker","labels_url":"https://api.github.com/repos/kaczmarj/neurodocker/issues/219/labels{/name}","comments_url":"https://api.github.com/repos/kaczmarj/neurodocker/issues/219/comments","events_url":"https://api.github.com/repos/kaczmarj/neurodocker/issues/219/events","html_url":"https://github.com/kaczmarj/neurodocker/issues/219","id":350463752,"node_id":"MDU6SXNzdWUzNTA0NjM3NTI=","number":219,"title":"Error using neurodocker reprozip","user":{"login":"xaviergp","id":24441807,"node_id":"MDQ6VXNlcjI0NDQxODA3","avatar_url":"https://avatars2.githubusercontent.com/u/24441807?v=4","gravatar_id":"","url":"https://api.github.com/users/xaviergp","html_url":"https://github.com/xaviergp","followers_url":"https://api.github.com/users/xaviergp/followers","following_url":"https://api.github.com/users/xaviergp/following{/other_user}","gists_url":"https://api.github.com/users/xaviergp/gists{/gist_id}","starred_url":"https://api.github.com/users/xaviergp/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/xaviergp/subscriptions","organizations_url":"https://api.github.com/users/xaviergp/orgs","repos_url":"https://api.github.com/users/xaviergp/repos","events_url":"https://api.github.com/users/xaviergp/events{/privacy}","received_events_url":"https://api.github.com/users/xaviergp/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2018-08-14T14:51:24Z","updated_at":"2018-08-14T15:54:27Z","closed_at":null,"author_association":"NONE","body":"Hi!\r\nI am trying to minimize a neurodocker container using neurodocker reprozip.\r\nMy container uses fsl, freesurfer, and HCPworkbench.\r\nI have a python script that takes a nifti file from the container and does some fsl, freesurfer, and HCPworkbench operations.\r\n\r\nI do this:\r\ndocker run --rm -itd --entrypoint bash --security-opt=seccomp:unconfined --name minify19 xaviergp/gradmap_forreprozip\r\nThen this:\r\nneurodocker reprozip trace -v debug minify19 \"python3 /src/gradmap_v1/toolbox_forreprozip.py\"\r\n\r\nI get this error, which does not appear when I run my container normally:\r\n[NEURODOCKER 2018-08-14 10:45:09,092 DEBUG]: ERROR:: Environment variable FSLOUTPUTTYPE is not set!\r\n[NEURODOCKER 2018-08-14 10:45:09,092 DEBUG]: Please make sure that the appropriate configuration file is sourced by your shell (e.g. by putting it in .profile).\r\n[NEURODOCKER 2018-08-14 10:45:09,092 DEBUG]: e.g. bash or sh users add the line \". ${FSLDIR}/etc/fslconf/fsl.sh\"\r\n[NEURODOCKER 2018-08-14 10:45:09,093 DEBUG]: e.g. tcsh or csh users add the line \"source ${FSLDIR}/etc/fslconf/fsl.csh\"\r\n\r\nDo you know what may be causing this?\r\nThank you,\r\nXavier."},"comment":{"url":"https://api.github.com/repos/kaczmarj/neurodocker/issues/comments/412921911","html_url":"https://github.com/kaczmarj/neurodocker/issues/219#issuecomment-412921911","issue_url":"https://api.github.com/repos/kaczmarj/neurodocker/issues/219","id":412921911,"node_id":"MDEyOklzc3VlQ29tbWVudDQxMjkyMTkxMQ==","user":{"login":"xaviergp","id":24441807,"node_id":"MDQ6VXNlcjI0NDQxODA3","avatar_url":"https://avatars2.githubusercontent.com/u/24441807?v=4","gravatar_id":"","url":"https://api.github.com/users/xaviergp","html_url":"https://github.com/xaviergp","followers_url":"https://api.github.com/users/xaviergp/followers","following_url":"https://api.github.com/users/xaviergp/following{/other_user}","gists_url":"https://api.github.com/users/xaviergp/gists{/gist_id}","starred_url":"https://api.github.com/users/xaviergp/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/xaviergp/subscriptions","organizations_url":"https://api.github.com/users/xaviergp/orgs","repos_url":"https://api.github.com/users/xaviergp/repos","events_url":"https://api.github.com/users/xaviergp/events{/privacy}","received_events_url":"https://api.github.com/users/xaviergp/received_events","type":"User","site_admin":false},"created_at":"2018-08-14T15:54:27Z","updated_at":"2018-08-14T15:54:27Z","author_association":"NONE","body":"Hi Jakub,\r\nThis is the full list of commands I used to build the neurodocker container:\r\n\r\ndocker.exe run --rm kaczmarj/neurodocker:master generate \"docker\" \\\r\n  --base=neurodebian:stretch-non-free \\\r\n  --pkg-manager=apt \\\r\n  --install connectome-workbench \\\r\n  --freesurfer version=6.0.0-min\\\r\n  --fsl version=5.0.11\\\r\n  --miniconda create_env=neuro \\\r\n  conda_install=\"python=3.6 numpy seaborn nibabel jupyter nilearn\" activate=true \\\r\n  pip_install=\"https://github.com/mgxd/niwidgets/archive/fix/inst.zip\" \\\r\n  --workdir='/src' \\\r\n  --user root \\\r\n  --run \"wget --output-document=gradmap.tar.gz https://www.dropbox.com/s/qrosgd80qrg9eiy/gradmap.tar.gz?dl=1 && tar -xvf gradmap.tar.gz && rm gradmap.tar.gz\" \\\r\n  --add-to-entrypoint=\"bash\" \\\r\n  --run \"mv /src/gradmap_v1/license.txt /opt/freesurfer-6.0.0-min/\" > dockerfile\r\n\r\ndocker.exe build -t gradmap_neurodocker_v21 .\r\n\r\nI pushed the container to dockerhub as xaviergp/gradmap_forreprozip, and then did this:\r\n\r\ndocker run --rm -itd --entrypoint bash --security-opt=seccomp:unconfined --name minify19 xaviergp/gradmap_forreprozip\r\n\r\nneurodocker reprozip trace -v debug minify19 \"python3 /src/gradmap_v1/toolbox_forreprozip.py\""}}
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