gget

npx skills add mturac/everything-openai-codex --skill scientific-pkg-gget --agent codex

Same command for any agent — swap --agent for claude-code, cursor, copilot.

# gget Use this skill when a task needs quick bioinformatics lookup across genomic reference databases with the `gget` CLI or Python package. ## When to Use - Finding Ensembl IDs, gene metadata, transcript details, or sequences. - Running quick BLAST or BLAT lookups without building a full local pipeline. - Fetching reference genome links and annotations from Ensembl. - Querying protein structure, pathway, cancer, expression, or disease-association modules through a single interface. - Creating a reproducible first-pass evidence log before moving to heavier tools such as Biopython, Snakemake, Nextflow, BLAST+, or database-specific clients. Use a dedicated workflow instead of `gget` when the task requires regulated clinical interpretation, high-throughput production pipelines, or fine-grained control over database versions and local indexes. ## Installation Use a clean Python environment. ```bash python -m venv .venv . .venv/bin/activate python -m pip install --upgrade pip python -m pip install --upgrade gget gget --help ``` If `uv` is available: ```bash uv venv . .venv/bin/activate uv pip install gget ``` Before relying on an older environment, upgrade `gget` and re-check the modul

python -m venv .venv
python -m pip install --upgrade pip
python -m pip install --upgrade gget
gget --help
uv venv
uv pip install gget
gget <module> [arguments] [options]
gget search -s human brca1 dna repair -o brca1-search.json
gget info ENSG00000012048 -o brca1-info.json
gget seq ENSG00000012048 -o brca1-seq.fa