phage-design

name	phage-design
description	Use when working from the local Evo 2 `phage_gen` project to design or analyze bacteriophage genomes, competition assays, or Gibson assembly fragments.
allowed-tools	["Read","Write","Bash(python:*)","Bash(docker:*)"]
context	fork
agent	bio-expert

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

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.