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GMOD / jb2hubs Public

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Shell script hardening#95

Merged

cmdcolin merged 11 commits intomainGMOD/jb2hubs:mainfrom

shell-script-hardeningGMOD/jb2hubs:shell-script-hardeningCopy head branch name to clipboard

Apr 13, 2026

Conversation Commits11 (11)Checks Files changed

Merged

Shell script hardening#95
cmdcolin merged 11 commits intomainfrom
shell-script-hardening

Commits

Commits on Apr 12, 2026

Website code quality fixes

cmdcolin
and
claude
committed
Harden shell scripts: set -euo pipefail, xxhash, safe var refs

cmdcolin
and
claude
committed
Restore || true for textIndexGoldenPath parallel call

cmdcolin
and
claude
committed
Fix createChainTrackPifs failing on assemblies with no liftOver chains

cmdcolin
and
claude
committed
Skip PIF generation for already-processed assemblies

cmdcolin
and
claude
committed

Commits on Apr 13, 2026

Format
cmdcolin
committed
Incremental file listing with XXH3: ~3x faster hashing

cmdcolin
and
claude
committed
Dry run output: remove bogus over.chain.gz liftOver tracks, reorder aggregateTextSearchAdapters

cmdcolin
and
claude
committed
Update
cmdcolin
committed
Fix defaultSession missing from minimal configs: run generateDefaultSessions before createMinimalConfigs

cmdcolin
and
claude
committed
Add set -euo pipefail to remaining ucsc2jbrowse scripts

cmdcolin
and
claude
committed

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