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conda-env

Create and update conda environment YAML files for Snakemake bioinformatics pipelines.

1|Updated Oct 25, 2020
Search Tags:#dependency management#HPC#bioinformatics#conda#Snakemake#bioconda#environment yaml
One-click install
npx skills add https://github.com/bfairkun/dotfiles --skill conda-env-bfairkun
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: conda-env
Source: https://github.com/bfairkun/dotfiles/tree/main/agents/.agents/skills/conda-env
Command: npx skills add https://github.com/bfairkun/dotfiles --skill conda-env-bfairkun

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve? Managing conda environments for Snakemake pipelines on the RCC Midway HPC cluster involves repetitive YAML editing, channel priority mistakes, and hard-to-diagnose build failures. This Skill standardizes how environment files in code/envs/ are created, updated, and debugged. ## Core Features & Use Cases - Standardized YAML format: Enforces the correct channel priority order (conda-forge, bioconda, defaults) and version pinning conventions for reproducible environments. - Package addition guidance: Provides a channel lookup table for common bioinformatics tools (samtools, STAR, salmon, bedtools) so packages land in the right channel with proper pins. - Build failure debugging: Supplies concrete commands for manual env creation, strict channel priority builds, and conda search to resolve unsolvable conflicts. - Use Case: When adding pysam to a rule-specific env, read the existing YAML, add the pinned dependency under the bioconda channel, and verify the build manually before Snakemake caches it. ## Quick Start Ask the AI to add the samtools package with a version pin to the conda environment YAML for your Snakemake rule.

Frequently Asked Questions about conda-env

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I add a package to an existing conda environment YAML?▼

Read the existing YAML first, then add the package under dependencies with a version pin. Use = for exact versions and >= for minimum versions, and prefer conda packages over pip when available for better dependency resolution.

What channel should I use for bioinformatics conda packages?▼

Most bioinformatics tools like samtools, bcftools, STAR, bwa, salmon, and bedtools are on the bioconda channel. General scientific Python packages like pandas, numpy, and scipy come from conda-forge.

Why does my conda environment build fail with unsolvable conflicts?▼

Unsolvable conflicts usually come from overly strict version pins or wrong channel priority. Try relaxing pins from = to >=, build with --strict-channel-priority, and ensure conda-forge is listed before bioconda and defaults.

How do I reference a conda environment in a Snakemake rule?▼

Add a conda directive pointing to the YAML path relative to the Snakefile, such as conda: "envs/myenv.yaml". Snakemake builds and caches the environment automatically on first use.

What can I do when conda environment builds take too long?▼

Slow builds are typically caused by the default dependency solver. Switch to the libmamba solver or use mamba instead of conda to speed up environment resolution significantly.

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