From 86c5ecfcc1d66a9b9c211f739e32c0a021e3455e Mon Sep 17 00:00:00 2001 From: Tim Dudgeon Date: Wed, 5 Aug 2026 14:02:20 +0100 Subject: [PATCH] fix: apt-get update before installing openbabel in Dockerfile-prep 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 Since bullseye-security periodically prunes superseded point-release .debs, that stale index eventually points at files that no longer exist, and the build starts failing with 404s - this is what was blocking jote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 --- Dockerfile-prep | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/Dockerfile-prep b/Dockerfile-prep index e47064f..be88843 100644 --- a/Dockerfile-prep +++ b/Dockerfile-prep @@ -8,7 +8,11 @@ FROM informaticsmatters/vs-rdkit-base:latest # openbabel does not install easily with PIP, and we don't have conda so we must use apt to install. # this installs version 3.1.1 -RUN apt-get -y install openbabel python3-openbabel &&\ +# apt-get update is required here (rather than relying on the base image's +# package index) because the bullseye-security mirror periodically prunes +# superseded point-release .debs, leaving a stale index full of 404s. +RUN apt-get -y update &&\ + apt-get -y install openbabel python3-openbabel &&\ apt-get clean ENV PYTHONPATH=/code