run-with-lock

name	run-with-lock
description	Use when wrapping a command in NCBI-style file locking so only one worker for a given lock base runs at a time.
disable-model-invocation	true
user-invocable	true

run-with-lock

Compiled NCBI helper for serializing a command behind a named lock. Binary strings and official NCBI source both confirm option names such as -base, -getter, -log, -map, and -reviewer, but this local installation is incomplete because the default get_lock helper is missing from PATH.

Quick Start

• Command: run_with_lock -base <lock-name> command [args...]
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/run_with_lock
• Observed dependency: external get_lock helper

When To Use This Tool

• Preventing two jobs with the same logical lock name from running concurrently
• Serializing fragile build, indexing, or cache-population steps
• Capturing a log file for a locked command run
• Reusing NCBI build-system locking conventions in custom workflows

Common Patterns

# Run one command behind a named lock
run_with_lock -base make_taxdb make taxdb

# Keep a lock-scoped log file
run_with_lock -base make_taxdb -log make_taxdb.log make taxdb

# Ignore the wrapped command's exit status after the lock is acquired
run_with_lock -base make_taxdb ! make taxdb

Recommended Workflow

1. Choose a stable lock base for the shared resource you are protecting.
2. Wrap the real command after any run_with_lock options.
3. Add -log when you want captured output, and only use ! when failure of the wrapped command should not propagate.
4. Verify that the supporting lock helper programs are actually installed before depending on this in production.

Guardrails

• --help and --version are not implemented as help/version paths here; local testing returned Unsupported option --help and Unsupported option --version.
• Bare invocation failed immediately with run_with_lock: Unable to exec get_lock: No such file or directory., so this environment is missing the default lock-getter helper.
• Binary strings plus official NCBI source confirm these parsed options: -base, -getter, -log, -map, -reviewer, plus a standalone ! marker that suppresses nonzero exit propagation from the wrapped command.
• If -base is omitted, the source derives it from the basename of the wrapped command and then forms <base>.lock.
• The source only applies -map remapping when the lock base begins with make_.