shell-script-executability-validation

shell-script-executability-validation

Summary

Verify that shell scripts within a cloned bioinformatics repository have correct permissions, dependencies, and can execute end-to-end on canonical input data to produce valid output. This skill validates the reproducibility of a computational workflow before relying on it for analysis.

When to use

You have cloned a bioinformatics repository (e.g., FredHutch/SEACR) and need to confirm that its shell and R scripts are executable and will run successfully on your input data (e.g., CUT&RUN bedGraph files) before investing time in a full analysis. Use this when the documentation is incomplete or untested, or when you need to audit an inherited workflow.

When NOT to use

• You are auditing code logic or algorithmic correctness beyond execution — this skill only validates end-to-end runtime, not statistical validity or method soundness.
• Input data is already pre-processed and integrated into a larger pipeline — use this skill on isolated workflows only.
• The repository provides pre-built binaries or Docker images; validation of binary executables and containers requires different QA practices.

Inputs

• cloned repository directory (via git clone)
• minimal test input file conforming to tool's documented format (e.g., bedGraph with zero-signal rows omitted)
• tool dependencies (R, Bedtools, or equivalents named in README)

Outputs

• validated shell scripts with executable permissions confirmed
• output BED file(s) conforming to documented schema
• execution logs (stdout/stderr) confirming no errors

How to apply

Clone the target repository using git. Inspect the cloned directory for shell scripts (.sh) and verify that execute permissions are set (chmod +x if needed). Prepare a minimal canonical input file that meets the tool's documented format requirements (e.g., a bedGraph file with chr, start, end, signal columns for SEACR). Execute the script end-to-end with the test input using the documented command-line syntax, capturing stdout and stderr. Verify that the expected output files are produced (e.g., .relaxed.bed or .stringent.bed) and that their structure matches the documented schema (e.g., chr, start, end, total signal, max signal, max signal region for SEACR). If execution succeeds and output schema is valid, the workflow is reproducible.