How do I install the Phage Design skill?

Run npx skillmds add vimalinx/phage-design 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 Phage Design safe to use?

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Which AI agents work with Phage Design?

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 Phage Design free to use?

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

Who published Phage Design?

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

Phage Design by vimalinx — Agent Skill

Name: Phage Design
Rating: 4.2 (5 reviews)
Author: vimalinx

File contents

phage-design

Project-specific gateway for /home/vimalinx/Projects/bio_studio/repositories/active/evo2/phage_gen. The local repo contains pipeline scripts, analysis utilities, environment YAMLs, and reference data for phage genome design, especially the genome design filtering workflow described in the subproject README.

Quick Start

Project root: /home/vimalinx/Projects/bio_studio/repositories/active/evo2/phage_gen
Main pipeline script: pipelines/genome_design_filtering_pipeline.py
Main config template: pipelines/genome_design_filtering_pipeline_config_template.yaml

When To Use This Tool

Running the local phage genome design filtering project
Analyzing phage competition experiments or designing Gibson assembly fragments
Working with the PhiX174 reference assets bundled in phage_gen/data/
Preparing phage-design experiments that depend on the Evo 2 local repo

Common Patterns

# Enter the local phage_gen project
cd /home/vimalinx/Projects/bio_studio/repositories/active/evo2/phage_gen

# Copy the config template, edit it, then run the Python pipeline directly
cp pipelines/genome_design_filtering_pipeline_config_template.yaml my_run.yaml
python pipelines/genome_design_filtering_pipeline.py my_run.yaml

# Run downstream analysis utilities
python analysis/competition_analysis.py
python analysis/genome_gibson_assembly.py

Recommended Workflow

Start from the phage_gen subproject, not from generic phage-design prose.
Read the local README and choose the relevant mode: genome-design filtering, competition analysis, Gibson assembly, or architecture visualization.
Copy and edit the bundled config template before launching the main pipeline.
Prepare the matching conda environments from environments/ if you want the full workflow rather than just code inspection.

Guardrails

The bundled genome_design_filtering_pipeline.sh is a Slurm template with literal /path/to/... placeholders. It is not runnable as-is.
The local README says you need conda environments derived from environments/genome_design.yaml and environments/genome_visualization.yaml.
This project is a phage-genome design subproject inside the Evo 2 repo, so any deeper Evo 2 runtime issues still apply.
Treat the bundled PhiX174 reference files and cited paper as examples/reference assets, not as proof that every target-host phage workflow is turnkey.

---name: phage-designdescription: Use when working from the local Evo 2 `phage_gen` project to design or analyze bacteriophage genomes, competition assays, or Gibson assembly fragments.--- # phage-design Project-specific gateway for `/home/vimalinx/Projects/bio_studio/repositories/active/evo2/phage_gen`. The local repo contains pipeline scripts, analysis utilities, environment YAMLs, and reference data for phage genome design, especially the genome design filtering workflow described in the subproject README. ## Quick Start - **Project root:** `/home/vimalinx/Projects/bio_studio/repositories/active/evo2/phage_gen` - **Main pipeline script:** `pipelines/genome_design_filtering_pipeline.py` - **Main config template:** `pipelines/genome_design_filtering_pipeline_config_template.yaml` ## When To Use This Tool - Running the local phage genome design filtering project - Analyzing phage competition experiments or designing Gibson assembly fragments - Working with the PhiX174 reference assets bundled in `phage_gen/data/` - Preparing phage-design experiments that depend on the Evo 2 local repo ## Common Patterns ```bash # Enter the local phage_gen project cd /home/vimalinx/Projects/bio_studio/repositories/active/evo2/phage_gen ``` ```bash # Copy the config template, edit it, then run the Python pipeline directly cp pipelines/genome_design_filtering_pipeline_config_template.yaml my_run.yaml python pipelines/genome_design_filtering_pipeline.py my_run.yaml ``` ```bash # Run downstream analysis utilities python analysis/competition_analysis.py python analysis/genome_gibson_assembly.py ``` ## Recommended Workflow 1. Start from the `phage_gen` subproject, not from generic phage-design prose. 2. Read the local README and choose the relevant mode: genome-design filtering, competition analysis, Gibson assembly, or architecture visualization. 3. Copy and edit the bundled config template before launching the main pipeline. 4. Prepare the matching conda environments from `environments/` if you want the full workflow rather than just code inspection. ## Guardrails - The bundled `genome_design_filtering_pipeline.sh` is a Slurm template with literal `/path/to/...` placeholders. It is not runnable as-is. - The local README says you need conda environments derived from `environments/genome_design.yaml` and `environments/genome_visualization.yaml`. - This project is a phage-genome design subproject inside the Evo 2 repo, so any deeper Evo 2 runtime issues still apply. - Treat the bundled PhiX174 reference files and cited paper as examples/reference assets, not as proof that every target-host phage workflow is turnkey.

Frequently asked questions