{"action":"created","issue":{"url":"https://api.github.com/repos/nextflow-io/nextflow/issues/755","repository_url":"https://api.github.com/repos/nextflow-io/nextflow","labels_url":"https://api.github.com/repos/nextflow-io/nextflow/issues/755/labels{/name}","comments_url":"https://api.github.com/repos/nextflow-io/nextflow/issues/755/comments","events_url":"https://api.github.com/repos/nextflow-io/nextflow/issues/755/events","html_url":"https://github.com/nextflow-io/nextflow/issues/755","id":333749320,"node_id":"MDU6SXNzdWUzMzM3NDkzMjA=","number":755,"title":"chown --from option unrecognized with non-GNU tools and fixOwnership on for Docker","user":{"login":"rspreafico-sgi","id":34698433,"node_id":"MDQ6VXNlcjM0Njk4NDMz","avatar_url":"https://avatars2.githubusercontent.com/u/34698433?v=4","gravatar_id":"","url":"https://api.github.com/users/rspreafico-sgi","html_url":"https://github.com/rspreafico-sgi","followers_url":"https://api.github.com/users/rspreafico-sgi/followers","following_url":"https://api.github.com/users/rspreafico-sgi/following{/other_user}","gists_url":"https://api.github.com/users/rspreafico-sgi/gists{/gist_id}","starred_url":"https://api.github.com/users/rspreafico-sgi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rspreafico-sgi/subscriptions","organizations_url":"https://api.github.com/users/rspreafico-sgi/orgs","repos_url":"https://api.github.com/users/rspreafico-sgi/repos","events_url":"https://api.github.com/users/rspreafico-sgi/events{/privacy}","received_events_url":"https://api.github.com/users/rspreafico-sgi/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2018-06-19T16:33:52Z","updated_at":"2018-06-20T15:51:02Z","closed_at":null,"author_association":"NONE","body":"When Docker containers that do not ship GNU tools are used (e.g. popular lightweight BusyBox, Alpine Linux, Biocontainers) and the `fixOwnership` option is on, `chown` fails due to the `--from` option being unsupported in non-GNU tools. \r\n\r\nTemporary workaround: set UID/GID in the Docker `runOptions`.\r\n\r\nPossible fixes:\r\n- have Nextflow set UID/GID for Docker if `fixOwnership` is on (as opposed to changing permissions after the run)\r\n- `chown` all output files, without pre-filtering on those owned by `root` (the Nextflow user should own all files anyway).\r\n\r\nReferenced from <https://github.com/nextflow-io/nextflow/issues/499#issuecomment-398461592>."},"comment":{"url":"https://api.github.com/repos/nextflow-io/nextflow/issues/comments/398800479","html_url":"https://github.com/nextflow-io/nextflow/issues/755#issuecomment-398800479","issue_url":"https://api.github.com/repos/nextflow-io/nextflow/issues/755","id":398800479,"node_id":"MDEyOklzc3VlQ29tbWVudDM5ODgwMDQ3OQ==","user":{"login":"rspreafico-sgi","id":34698433,"node_id":"MDQ6VXNlcjM0Njk4NDMz","avatar_url":"https://avatars2.githubusercontent.com/u/34698433?v=4","gravatar_id":"","url":"https://api.github.com/users/rspreafico-sgi","html_url":"https://github.com/rspreafico-sgi","followers_url":"https://api.github.com/users/rspreafico-sgi/followers","following_url":"https://api.github.com/users/rspreafico-sgi/following{/other_user}","gists_url":"https://api.github.com/users/rspreafico-sgi/gists{/gist_id}","starred_url":"https://api.github.com/users/rspreafico-sgi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rspreafico-sgi/subscriptions","organizations_url":"https://api.github.com/users/rspreafico-sgi/orgs","repos_url":"https://api.github.com/users/rspreafico-sgi/repos","events_url":"https://api.github.com/users/rspreafico-sgi/events{/privacy}","received_events_url":"https://api.github.com/users/rspreafico-sgi/received_events","type":"User","site_admin":false},"created_at":"2018-06-20T15:51:02Z","updated_at":"2018-06-20T15:51:02Z","author_association":"NONE","body":"In my case, using UID and GID in runOptions works really well."}}
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