Install headless Chrome in Docker image for QC plot rendering - #27
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m-reuter merged 1 commit intoAug 6, 2026
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kaleido>=1.0 dropped its bundled Chromium and now requires an external Chrome/Chromium binary to render QC plots, which the Docker image did not provide (Kaleido requires Google Chrome to be installed). Install Chrome via plotly_get_chrome into a fixed, world-readable location and point to it via BROWSER_PATH, since the image is meant to be run with an arbitrary --user; also default HOME to a writable directory, since Chrome needs a writable profile/user-data directory. Verified by building the image from this Dockerfile and running the full pipeline (mesh/profile/hull QC stages) both as root and as an arbitrary non-root --user, producing valid PNGs in all three cases with no warnings. Refs Deep-MI#24
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Summary
Follow-up to #24 / #26, per @m-reuter's suggestion to fix the Docker image directly as a stopgap until a kaleido replacement is decided on.
kaleido>=1.0(currently pinned askaleido>=0.2.1, and1.3.0in the published0.10.1image) dropped its bundled Chromium and now requires an external Chrome/Chromium binary, whichdocker/Dockerfilenever installed.plotly_get_chromehelper into a fixed, world-readable location (/opt/chrome-for-testing), and points to it via theBROWSER_PATHenv var kaleido/choreographer respects.HOME=/tmp.Both of these are needed specifically because this image is documented to be run with an arbitrary
--user XXXX:YYYY(seedocker/Docker.md): installing Chrome to the default$HOME(root's, at build time) is unreadable to an arbitrary non-root UID at runtime, and Chrome needs a writable profile/user-data directory, which an arbitrary UID won't have without a saneHOMEdefault.docker/Docker.md: removed the now-stale--no-qcfrom the example command and the note saying QC isn't supported under Docker/Singularity, and added a short note for local (non-Docker) installs on how to get Chrome viaplotly_get_chrome.Test plan
Built the image from this
Dockerfilefrom scratch and ran the full pipeline against a real hippocampal segmentation, both as root and as an arbitrary non-root--user(matching the documented invocation):docker buildrun_hipsta) completes withHipsta finished without errors.--user UID:GIDwith no manual-e HOME=...override (i.e. out-of-the-box with just the Dockerfile changes)