{"id":18565637,"url":"https://github.com/quiltdata/omics-quilt-demo","last_synced_at":"2026-02-17T23:31:37.137Z","repository":{"id":210797975,"uuid":"727475946","full_name":"quiltdata/omics-quilt-demo","owner":"quiltdata","description":"Use CDK to create Quilt packages from AWS HealthOmics","archived":false,"fork":false,"pushed_at":"2025-04-01T01:59:07.000Z","size":972,"stargazers_count":0,"open_issues_count":5,"forks_count":0,"subscribers_count":4,"default_branch":"main","last_synced_at":"2025-04-08T14:11:12.365Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"TypeScript","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/quiltdata.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2023-12-04T23:59:13.000Z","updated_at":"2024-12-20T20:11:10.000Z","dependencies_parsed_at":"2024-01-16T21:49:04.357Z","dependency_job_id":"aa89a793-46ca-4cfe-b7d3-963932175f93","html_url":"https://github.com/quiltdata/omics-quilt-demo","commit_stats":null,"previous_names":["quiltdata/omics-quilt-demo"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/quiltdata/omics-quilt-demo","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/quiltdata%2Fomics-quilt-demo","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/quiltdata%2Fomics-quilt-demo/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/quiltdata%2Fomics-quilt-demo/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/quiltdata%2Fomics-quilt-demo/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/quiltdata","download_url":"https://codeload.github.com/quiltdata/omics-quilt-demo/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/quiltdata%2Fomics-quilt-demo/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29562195,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-17T21:50:49.831Z","status":"ssl_error","status_checked_at":"2026-02-17T21:46:15.313Z","response_time":100,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.6:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-11-06T22:19:36.848Z","updated_at":"2026-02-17T23:31:37.107Z","avatar_url":"https://github.com/quiltdata.png","language":"TypeScript","funding_links":[],"categories":[],"sub_categories":[],"readme":"# omics-quilt-demo\n\nUse CDK to create Quilt packages from AWS HealthOmics\n\n## Usage\n\n### Installation\n\nUse CDK to create and deploy the stack.\nNote that it requires a large Cloud9 instance to run Docker.\n\n```bash\ncp example.env .env # and edit\nsource .env\naws configure list-profiles # verify AWS credentials exist\n# npx npm install # if npm not present (but npx is)\nnpm install yarn -g # if yarn not present (but npm is)\nyarn install\n# set bootstrap region (if new or changed)\nnpx cdk bootstrap aws://$CDK_DEFAULT_ACCOUNT/$CDK_DEFAULT_REGION\n# start Docker if not already running\nsudo systemctl start docker # e.g. on Linux (requires large Cloud9 instance!)\nnpm run deploy\n```\n\nYou will also need to accept the Subscription from your email client.\n\n#### Note: macOS fails on docker-credential-helper\n\nIf running on macOS, you will get an error for `docker-credentials-helper`.\nYou will need to install and alias that and the `docker-credential-desktop` helper.\n\n```bash\nbrew install docker-credential-helper\ncd /opt/homebrew/bin\nln -s docker-credential-osxkeychain docker-credential-helper\nln -s docker-credential-osxkeychain docker-credential-desktop\n```\n\n### Quilt Integration\n\nUse your Quilt Catalog to browse the inputs and outputs\n\n1. Go to AWS Console and find the Omics-Quilt stack\n   1. Copy names of the INPUT and OUTPUT buckets\n   2. Copy the SNS Topic ARN, with type \"AWS::SNS::Topic\", e.g. `arn:aws:sns:us-east-1:1234567890:omics-quilt-status-topic`\n2. Go your Quilt Catalog\n3. Click \"+\" on the front page (or Admin Settings -\u003e Buckets)\n4. Click \"+\" in the upper right corner to add a new bucket\n   1. Name: Physical Name from Stack\n   2. Title: Omics Quilt Input / Output\n   3. SNS Topic ARN (under Indexing and Notifications)\n\n### Run the Workflow\n\n1. Find or create your region's input parameters file: `./workflows/fastq/\u003cregion\u003e.json`\n2. Go to Console and find the input bucket\n3. Create Folders `fastq` and, inside that, `\u003cregion\u003e`\n4. Upload the JSON file to `s3://\u003cinput-bucket\u003e/fastq/\u003cregion\u003e/\u003cregion\u003e.json`\n\nIf it already exists, set the timestamp to a future time to trigger a new run.\n\nTODO: Setup a Quilt package push that does this for you\n\n### View the Results\n\n1. Go to the 'packager' Lambda and view the logs\n2. Grab the 'quilt+uri' from the output\n3. Paste into the URI field of the Quilt Catalog (next to the search bar)\n   1. NOTE: May need to click the package name to stop page reloading\n4. Click \"Expand\" (and tripledot menu) to interact with result DataGrids\n\n## Development\n\nUses [pre-commit](https://pre-commit.com/) to pre-lint files.\n\n```bash\npre-commit install\npre-commit run --all-files\n```\n\nUses [projen](https://github.com/projen/projen) to manage project files.\n\n```bash\nyarn install\nnpm run projen\nnpm run eslint\nnpm run build\nnpm run test:watch\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fquiltdata%2Fomics-quilt-demo","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fquiltdata%2Fomics-quilt-demo","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fquiltdata%2Fomics-quilt-demo/lists"}