run-ncbi-converter

name	run-ncbi-converter
description	Use when launching an NCBI converter binary through the `run-ncbi-converter` wrapper that downloads and caches the platform-specific executable on demand.
disable-model-invocation	true
user-invocable	true

run-ncbi-converter

Perl bootstrap wrapper from Entrez Direct. It does not perform the conversion itself; instead it infers the current platform, downloads a named converter binary from NCBI FTP into a cache directory, unpacks it, and then execs that converter with the remaining arguments.

Quick Start

• Command: run-ncbi-converter <converter-name> [converter-args...]
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/run-ncbi-converter
• Default cache directory: ~/.cache/ncbi-converters

When To Use This Tool

• Bootstrapping one of the NCBI converter binaries without manually downloading it first
• Reusing cached platform-specific converter executables across repeated runs
• Redirecting converter downloads into a controlled cache directory via NCBI_CONVERTER_DIR
• Debugging why an Entrez Direct converter wrapper is failing before the actual converter starts

Common Patterns

# Run a named converter through the bootstrap wrapper
run-ncbi-converter <converter-name> [converter-args...]

# Keep downloaded converters in a project-local cache
export NCBI_CONVERTER_DIR="$PWD/.ncbi-converters"
run-ncbi-converter <converter-name> [converter-args...]

# Inspect or clean the cache between runs
ls ~/.cache/ncbi-converters

Recommended Workflow

1. Decide which converter binary you actually need; the first positional argument becomes the remote archive basename.
2. Optionally point NCBI_CONVERTER_DIR at a writable cache location.
3. Run the wrapper only when FTP access to ftp.ncbi.nlm.nih.gov is available.
4. If the bootstrap succeeds, treat everything after the first argument as arguments for the downloaded converter, not for the wrapper itself.

Guardrails

• There is no local --help or --version path: passing -h or --version is interpreted as a converter name and immediately triggers FTP access.
• In this workspace, invoking the wrapper failed before any conversion with Unable to connect to FTP server: Bad file descriptor.
• The source hardcodes ftp.ncbi.nlm.nih.gov and a per-platform directory under /toolbox/ncbi_tools/converters/by_platform/.
• On Unix-like systems the wrapper downloads <converter>.<platform>.gz, runs gunzip -n, renames the unpacked file to the bare converter name, marks it executable, and then execs it.
• If you do not provide a first positional argument, the wrapper still constructs an archive name from $ARGV[0], so empty or malformed invocations are not gracefully handled.