| name | ref-cache |
| description | Use when managing local reference sequence caches for htslib-based tools. Invokes the ref-cache CLI to configure or interact with reference cache directories. |
| disable-model-invocation | true |
| user-invocable | true |
ref-cache
ref-cache is an HTSlib reference-caching proxy for CRAM workflows. It serves MD5-addressed reference sequence requests from a local cache, optionally fetching missing sequences from an upstream refget-like service.
Quick Start
- Command:
ref-cache [options] -d <cache_dir>
- Local executable:
/home/vimalinx/miniforge3/envs/bio/bin/ref-cache
- Local help path:
ref-cache -h
When To Use This Tool
- Managing local caches of reference sequences in htslib-based workflows
- Configuring cache directories for reference data access
- Running a local CRAM reference proxy instead of repeatedly hitting a remote server
- Wiring
REF_PATH to a local cache plus HTTP fallback
Common Patterns
mkdir -p cached_refs logs
ref-cache -b -d cached_refs -l logs -p 8080 -u https://www.ebi.ac.uk/ena/cram/md5/
ref-cache -d cached_refs -U -p 8080
export REF_PATH='/abs/path/cached_refs/%2s/%2s/%s:http:://myhost::8080/%s'
Recommended Workflow
- Create the cache and log directories first.
- Decide whether the service should run in the foreground, as a daemon (
-b), or under systemd socket activation (-s).
- Choose whether to allow upstream fetches (
-u) or serve only local files (-U).
- After startup, wire the service into CRAM tooling via
REF_PATH.
Guardrails
-d <dir> is mandatory.- This tool uses short options only in local testing.
-h shows help, while --help / --version were not validated as safe paths.
- The man page says
-b and -s are mutually exclusive.
- According to the man page,
ref-cache exits silently if it detects another instance already listening on the chosen port.
-U disables upstream fetches entirely; without it, the default upstream is https://www.ebi.ac.uk/ena/cram/md5/.
