fix: redirect HOME to /tmp in Nextflow env so ChimeraX can write its data dir#104
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…ingularity ChimeraX initializes a per-user data dir at \$HOME/.chimerax/ on first invocation. Singularity passes the host \$HOME through to the container; on most clusters that path is read-only inside the container, so ChimeraX fails with "Unable to make user's data directory: Read-only file system" and silently produces no PNG output during chimerax-plot. Override HOME=/tmp at the pipeline env level (mirroring the workaround already used in deepCSA) so ChimeraX has a writable home regardless of host config. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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Pull request overview
This PR updates the Nextflow pipeline configuration to ensure ChimeraX can initialize its per-user data directory inside containerized runs by redirecting HOME to a writable location (/tmp), addressing failures on clusters where the container-visible $HOME is not writable.
Changes:
- Add
HOME=/tmpto the pipeline-wideenv {}block innextflow.config. - Document the rationale for redirecting
HOME(ChimeraX writes~/.chimeraxon first run).
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Summary
ChimeraX initializes a per-user data dir at
$HOME/.chimerax/on first invocation. Singularity passes the host$HOMEthrough to the container; on most clusters that path is read-only inside the container, so ChimeraX fails withUnable to make user's data directory: Read-only file systemand silently produces no PNG output duringchimerax-plot.Override
HOME=/tmpat the pipelineenvlevel so ChimeraX has a writable home regardless of host config.