Interactive bioinformatics command-line tutorials.
dev: Development branch, pushing there runs tests if changes to app/* were made + auto deploys to dev.sandbox.biomain: Production branch; merge dev into main to deploy to stg.sandbox.bio
npm run devnpm run testwill launch all the tests in headless waycypress openopens Cypress so you can see the tests inside Chromenpm run test -- --spec "tests/test_tutorials.js"runs a single file
npm run deploy-dev// Terminal.svelte
const TOOLS_DEFAULT = [{
tool: "samtools",
version: "1.10",
urlPrefix: "http://localhost:12346/biowasm/tools/samtools/build/"
}];// cli.js
_aioli = await new Aioli(config.tools, {
env: window.location.hostname == "localhost" ? "stg" : "prd",
debug: window.location.hostname == "localhost",
urlAioli: "http://localhost:12346/aioli/dist/aioli.worker.js"
});<script>
import Quiz from "components/Quiz.svelte";
import Choice from "components/QuizChoice.svelte";
</script>
<!-- The "id" is used to maintain state on page refresh. It just has to be unique within a step in a tutorial -->
<Quiz id="q1" choices={[
{ valid: true, value: "Shell"},
{ valid: false, value: "Terminal"},
]}>
<span slot="prompt">
Is Bash a shell or a terminal?
</span>
</Quiz>
<Quiz id="q2" choices={[
{ valid: true, value: "ls -s -h Data"},
{ valid: true, value: "ls -sh Data"},
{ valid: false, value: "ls -size -h Data"},
{ valid: true, value: "ls --size -h Data"},
{ valid: false, value: "ls --sizeh Data"},
{ valid: false, value: "ls --size-h Data"},
{ valid: true, value: "ls -h -s Data"},
{ valid: true, value: "ls -hs Data"},
{ valid: false, value: "ls -hsize Data"},
]}>
<span slot="prompt">
Among the following commands, which ones are correct?
</span>
</Quiz>
<Quiz id="q3" choices={[
{ valid: true, value: "yes"},
{ valid: false, value: "no"},
]}>
<span slot="prompt">
Now, type the following command in your terminal and then press <kbd>Enter</kbd> key: `date`
Does the terminal display the current date?
</span>
</Quiz>| Environment | Domain | Access |
|---|---|---|
| dev | dev.sandbox.bio | Only me |
| stg | stg.sandbox.bio | Testers |
| prd | [prd.]sandbox.bio | Public |
| Environment variable | Description |
|---|---|
SUPABASE_URL |
Supabase URL |
SUPABASE_API_KEY |
Supabase database admin key |
| Table | Description | Access |
|---|---|---|
| logs | Log all calls to sandbox.bio/* |
RLS |
| pings | Analytics for tutorial progress | RLS |
| state | Save environment variables and tutorial progress | RLS |
Append _stg to table names for dev/stg environments.