How do I install the Transmute skill?

Run npx skillmds add vimalinx/transmute in your terminal (requires Node.js), paste this page's agent-chat prompt into Claude, Cursor, or any MCP-connected agent, or download the SKILL.md file and copy it into your agent's skills directory.

Is Transmute safe to use?

This skill has not completed SkillMD's automated safety review yet. Capability flags: docs only. SkillMD never runs a skill's scripts for you; review the SKILL.md before installing.

Which AI agents work with Transmute?

This skill is tagged as working with Claude Code, Claude.ai, OpenAI Codex. SKILL.md is an open format, so most agents that read a skills directory can load it too.

Is Transmute free to use?

Yes. Installing skills from SkillMD is free, and the skill stays under its author's original license.

Who published Transmute?

vimalinx (@vimalinx) published this skill. Their other Agent Skills are listed on their SkillMD profile.

Transmute by vimalinx — Agent Skill

Name: Transmute
Rating: 4.5 (4 reviews)
Author: vimalinx

File contents

transmute

Public wrapper script for the NCBI transmute toolkit. Some modes are handled directly in shell, Perl, Python, or xmllint helpers, while the remaining arguments are passed through to the compiled platform-specific executable such as transmute.Linux.

Quick Start

Command: transmute [options]
Local executable: /home/vimalinx/miniforge3/envs/bio/bin/transmute
Platform backend here: transmute.Linux

When To Use This Tool

Using the preferred public transmute entry point instead of calling the platform binary directly
Running format-conversion or sequence-processing modes described in transmute -help
Accessing shell-intercepted convenience modes such as -j2p, -x2p, -sort-by-length, or XML encode/decode helpers
Building pipelines that should stay portable across platforms because the wrapper selects the correct compiled backend

Common Patterns

# Convert JSON to XML through the public wrapper
printf '{"a":1}\n' | transmute -j2x -set Set -rec Rec

# Pretty-print JSON using the wrapper's python helper path
printf '{"a":1}\n' | transmute -j2p

# Wrapper-level line-length sort helper
printf 'bbb\na\ncc\n' | transmute -sort-by-length

Recommended Workflow

Start with transmute -help to choose the right mode.
Prefer the wrapper over transmute.Linux when you want portability or wrapper-only helper modes.
Feed data through stdin unless the selected mode explicitly documents file-based arguments.
If a mode behaves oddly, check whether it is one of the shell-intercepted paths before blaming the compiled backend.

Guardrails

transmute -help and transmute -version both work here and report version 24.0.
The wrapper intercepts several modes itself, including -encodeXML, -decodeXML, -plainXML, -x2p, -j2p, -x2j, -word-pairs, -sort-by-length, and multiple newline-conversion helpers.
Some intercepted modes have extra runtime dependencies: for example -x2p needs xmllint, -j2p needs python3, and several helpers require perl.
In local testing, printf '{"a":1}\n' | transmute -j2x -set Set -rec Rec produced a wrapped XML document with <Set><Rec><a>1</a></Rec></Set>.
If the compiled backend is missing, the wrapper prints explicit download instructions for transmute.<platform>.gz rather than failing silently.

---name: transmutedescription: Use when invoking the public `transmute` wrapper for format conversion, sequence editing, or shell-level helper modes that may be intercepted before dispatch to the platform binary.--- # transmute Public wrapper script for the NCBI `transmute` toolkit. Some modes are handled directly in shell, Perl, Python, or `xmllint` helpers, while the remaining arguments are passed through to the compiled platform-specific executable such as `transmute.Linux`. ## Quick Start - **Command:** `transmute [options]` - **Local executable:** `/home/vimalinx/miniforge3/envs/bio/bin/transmute` - **Platform backend here:** `transmute.Linux` ## When To Use This Tool - Using the preferred public `transmute` entry point instead of calling the platform binary directly - Running format-conversion or sequence-processing modes described in `transmute -help` - Accessing shell-intercepted convenience modes such as `-j2p`, `-x2p`, `-sort-by-length`, or XML encode/decode helpers - Building pipelines that should stay portable across platforms because the wrapper selects the correct compiled backend ## Common Patterns ```bash # Convert JSON to XML through the public wrapper printf '{"a":1}\n' | transmute -j2x -set Set -rec Rec ``` ```bash # Pretty-print JSON using the wrapper's python helper path printf '{"a":1}\n' | transmute -j2p ``` ```bash # Wrapper-level line-length sort helper printf 'bbb\na\ncc\n' | transmute -sort-by-length ``` ## Recommended Workflow 1. Start with `transmute -help` to choose the right mode. 2. Prefer the wrapper over `transmute.Linux` when you want portability or wrapper-only helper modes. 3. Feed data through stdin unless the selected mode explicitly documents file-based arguments. 4. If a mode behaves oddly, check whether it is one of the shell-intercepted paths before blaming the compiled backend. ## Guardrails - `transmute -help` and `transmute -version` both work here and report version `24.0`. - The wrapper intercepts several modes itself, including `-encodeXML`, `-decodeXML`, `-plainXML`, `-x2p`, `-j2p`, `-x2j`, `-word-pairs`, `-sort-by-length`, and multiple newline-conversion helpers. - Some intercepted modes have extra runtime dependencies: for example `-x2p` needs `xmllint`, `-j2p` needs `python3`, and several helpers require `perl`. - In local testing, `printf '{"a":1}\n' | transmute -j2x -set Set -rec Rec` produced a wrapped XML document with `<Set><Rec><a>1</a></Rec></Set>`. - If the compiled backend is missing, the wrapper prints explicit download instructions for `transmute.<platform>.gz` rather than failing silently.

Frequently asked questions