| name | download-ncbi-software |
| description | Use when fetching a small set of NCBI command-line binaries (`magic-blast`, `datasets`, or `sra-toolkit`) with the bundled EDirect downloader. |
| disable-model-invocation | true |
| user-invocable | true |
download-ncbi-software
Quick Start
- Command:
download-ncbi-software [ magic-blast | datasets | sra-toolkit ]
- Local executable:
/home/vimalinx/miniforge3/envs/bio/bin/download-ncbi-software
- Full reference: See
references/help.md
When To Use This Tool
- Download
magic-blast, datasets / dataformat, or sra-toolkit directly from NCBI-hosted distribution locations.
- Grab platform-specific binaries without manually browsing the FTP / HTTPS directories.
- Bootstrap a local tool directory in shell-heavy EDirect workflows.
Common Patterns
PATH=/home/vimalinx/miniforge3/envs/bio/bin:$PATH \
/home/vimalinx/miniforge3/envs/bio/bin/download-ncbi-software magic-blast
PATH=/home/vimalinx/miniforge3/envs/bio/bin:$PATH \
/home/vimalinx/miniforge3/envs/bio/bin/download-ncbi-software datasets
/home/vimalinx/miniforge3/envs/bio/bin/download-ncbi-software --help
Recommended Workflow
- Decide whether you need
magic-blast, datasets, or sra-toolkit.
- Run the downloader from the directory where you want the files to land.
- Verify that the expected executable or unpacked directory actually appeared.
- Add execute permissions or move the downloaded binaries into your normal tool path if needed.
Guardrails
- This script only knows three package families:
magic-blast, datasets / dataformat, and sra-toolkit.
- It depends on the EDirect helper
nquire; keep the bio / EDirect bin directory on PATH.
- Platform support is uneven. In the current Linux x86_64 source logic,
magic-blast and datasets are handled, but sra-toolkit falls through with an empty suffix and effectively does nothing while still exiting successfully.
- The downloads unpack into the current working directory; this is an operational script, not a dry-run metadata query.
