Scripts¶
Root-level script wrappers have been removed. Use categorized paths directly.
| Category | Path | Purpose |
|---|---|---|
| Environment | scripts/env/ |
Conda/bootstrap/install scripts |
| Operations | scripts/ops/ |
background runs, monitors, production helpers |
| Maintenance | scripts/maintenance/ |
VEP/reference/dependency maintenance |
| Diagnostics | scripts/diagnostics/ |
structure/API checks and debug probes |
| Experiments | scripts/experiments/ |
benchmark and overnight experiment runners |
| Development | scripts/dev/ |
demos, plotting checks, local tests |
Common Scripts¶
scripts/env/install.sh # visualizer env (bcftools, samtools, [visualizer]); --training, --alphagenome-server, --no-conda
source scripts/env/start_genomics_universal.sh
scripts/env/install_genomics_env.sh # full bioinformatics toolchain for genomes-analyzer
source scripts/maintenance/vep_install.sh
scripts/ops/run_in_background.sh --config configs/genomes_analyzer/config_human_30x_latest_ref.yaml
scripts/ops/monitor_monster.sh
scripts/diagnostics/diagnose_bcftools_error.sh
python3 scripts/dev/capture_docs_screenshots.py --url http://127.0.0.1:8780/ # retake the docs screenshots from a running visualizer
capture_docs_screenshots.py drives the visualizer in headless Chromium (Playwright) and writes the
WebP screenshots and figures under docs/assets/visualizer/. The shots follow the tutorial's
running example on 1kg_high_coverage. Some need an AlphaGenome backend (Perturbation Lab,
expression in other tissues), a loadable trained run, and network access for GTEx, Ensembl and
ENCODE. --list shows the shots and --only a,b retakes some.