fix: apt-get update before installing openbabel in Dockerfile-prep - #23
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Dockerfile-prep never ran apt-get update itself, relying on the package index baked into informaticsmatters/vs-rdkit-base:latest at base-image build time. Since bullseye-security periodically prunes superseded point-release .debs, that stale index eventually points at files that no longer exist, and the build starts failing with 404s - this is what was blocking jote for open3dalign, sucos, assemble_conformers, cluster_butina, enumerate, le_conformers, rdkit_dedup, rdkit_props, sa_score, screen and reactor after #21/#22. No version is pinned for openbabel here, so a fresh apt-get update resolves to whatever build is currently on the mirror instead (still 3.1.1, just a different point release). Verified: image builds; full im-virtual-screening/rdkit/xchem jote suite passes 32/32 (with NXF_VER=22.10.0 per docs/testing-jobs.md, for the nextflow-based jobs in the same suite). Part of #18. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
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Summary
Dockerfile-prepnever ranapt-get updateitself — it relied on the package index baked intoinformaticsmatters/vs-rdkit-base:latestat base-image build time.bullseye-securityperiodically prunes superseded point-release.debs, so that stale index eventually points at files that no longer exist, and the build starts failing with 404s. This was blockingjoteforopen3dalign,sucos,assemble_conformers,cluster_butina,enumerate,le_conformers,rdkit_dedup,rdkit_props,sa_score,screenandreactorafter #21/#22 — confirmed it also fails identically on pre-migration code, so it's unrelated to theim-rdkit-utilitiesmigration itself, just something that surfaced while verifying it.No version is pinned for
openbabel/python3-openbabelhere, so a freshapt-get updateresolves to whatever build is currently on the mirror instead (still3.1.1+dfsg-6, just resolved fresh rather than from a stale cached index).Test plan
im-virtual-screening/rdkit/xchemjotesuite passes 32/32 (withNXF_VER=22.10.0perdocs/testing-jobs.md, needed for the nextflow-based jobs in the same suite — unrelated to this change)🤖 Generated with Claude Code