Quick Start

Prerequisites

Node.js ≥ 18
ata for local task execution (../ata)
annotask for qsubsge cluster submission (../annotask) — optional if all tasks use executor: local

npm install -g @seqyuan/annopi

Or with pnpm:

pnpm add -g @seqyuan/annopi

Verify:

annopi --help

The repo includes fixtures copied from Python annopi:

annopi conf \
  -p tests/fixtures/annopi/pipeline.yml \
  -c tests/fixtures/annopi/project.yml \
  -o /tmp/annopi-out

This generates:

/tmp/annopi-out/
├── shell/
│   ├── 1-0-cellranger.sh
│   └── 2-0-qc.sh
└── tasks.yml

Inspect the output:

cat /tmp/annopi-out/tasks.yml

Then execute:

annopi run -o /tmp/annopi-out

Completed tasks write a .sign file under shell/. Re-running annopi run skips done tasks.

Clone the monorepo if you want to work on annopi-ts itself:

git clone https://github.com/seqyuan/annopi-ts.git
cd annopi-ts
pnpm install
pnpm build
pnpm test
pnpm typecheck

Link the local CLI:

cd packages/cli
npm link
cd ../..
annopi conf -p ... -c ... -o ...

pnpm site:dev

Open http://localhost:3000 for the English home page, or http://localhost:3000/zh for Chinese.