| name | nhance-sh |
| description | Use when trying the `nhance.sh` shortcut wrapper around `nquire` for pathway, gene-to-pathway, LitVar, or citation-match lookups against NCBI-related endpoints. |
| disable-model-invocation | true |
| user-invocable | true |
nhance-sh
Quick Start
- Command:
nhance.sh <shortcut> <query>
- Local executable:
/home/vimalinx/miniforge3/envs/bio/bin/nhance.sh
- Supported shortcuts from the local source:
-pathway, -gene-to-pathway, -litvar, -citmatch
When To Use This Tool
- Try the packaged shortcut wrapper for a few common
nquire-based lookups.
- Resolve a Reactome pathway, gene-to-pathway mapping, LitVar entity, or heuristic citation match without building the raw
nquire call yourself.
- Prototype an EDirect-side lookup quickly before deciding whether a lower-level
nquire command is more reliable.
- Not for general-purpose EDirect requests; this wrapper only special-cases four shortcut modes.
Common Patterns
nhance.sh -pathway Reactome:R-HSA-70171
nhance.sh -gene-to-pathway 1956
nhance.sh -citmatch "nucleotide sequences required for tn3 transposition immunity"
Recommended Workflow
- Decide whether your request really matches one of the four hard-coded shortcut modes.
- Pass exactly one query argument after the shortcut flag.
- Inspect the returned XML or PMID-style result and fall back to raw
nquire if you need tighter control.
- Treat this wrapper as a convenience layer, not as the authoritative interface for complex EDirect querying.
Guardrails
- The wrapper has no real built-in help or version path;
nhance.sh --help exits silently with no useful output.
- Only
-pathway, -gene-to-pathway, -litvar, and -citmatch are recognized as active shortcut modes.
- Missing shortcut payloads fail explicitly, for example
ERROR: Missing -pathway argument.
- In the current local environment, active shortcut calls fail early with
Escape: command not found, so the wrapper is not presently reliable without that missing shell helper.
- Plain
nhance.sh or unrecognized leading arguments can exit successfully with no output at all, which makes silent failure easy to miss.
- Successful use also depends on
nquire, transmute, and xtract being on PATH, plus live network access to the underlying NCBI / PubChem endpoints.
