{"id":18583317,"url":"https://github.com/alexpreynolds/tabix-service","last_synced_at":"2025-09-14T14:41:05.794Z","repository":{"id":75268389,"uuid":"92542770","full_name":"alexpreynolds/tabix-service","owner":"alexpreynolds","description":"A nodejs-based service for requests for tabix-indexed genomic data","archived":false,"fork":false,"pushed_at":"2019-11-12T20:38:57.000Z","size":127,"stargazers_count":2,"open_issues_count":1,"forks_count":4,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-09-09T03:52:05.186Z","etag":null,"topics":["bioinformatics","genomics","genomics-visualization","nodejs","samtools","tabix","web-service"],"latest_commit_sha":null,"homepage":null,"language":"JavaScript","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/alexpreynolds.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":"2017-05-26T19:35:40.000Z","updated_at":"2020-07-11T09:36:59.000Z","dependencies_parsed_at":"2023-06-05T23:30:34.398Z","dependency_job_id":null,"html_url":"https://github.com/alexpreynolds/tabix-service","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/alexpreynolds/tabix-service","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/alexpreynolds%2Ftabix-service","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/alexpreynolds%2Ftabix-service/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/alexpreynolds%2Ftabix-service/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/alexpreynolds%2Ftabix-service/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/alexpreynolds","download_url":"https://codeload.github.com/alexpreynolds/tabix-service/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/alexpreynolds%2Ftabix-service/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":275119146,"owners_count":25408749,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","status":"online","status_checked_at":"2025-09-14T02:00:10.474Z","response_time":75,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"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":["bioinformatics","genomics","genomics-visualization","nodejs","samtools","tabix","web-service"],"created_at":"2024-11-07T00:21:52.082Z","updated_at":"2025-09-14T14:41:05.786Z","avatar_url":"https://github.com/alexpreynolds.png","language":"JavaScript","funding_links":[],"categories":[],"sub_categories":[],"readme":"# tabix-service\nA nodejs-based service for requests for tabix-indexed genomic data\n\n## Prerequisites\n\nThese instructions assume a CentOS 7 host and sudo-level access. It's probably easiest to set up a virtual host and run these tests within that host.\n\n### `htslib` toolkit\n\nTo set up `htslib` (and `bgzip` and `tabix` tools):\n\n```\n$ git clone git://github.com/samtools/htslib.git\n$ git clone git://github.com/samtools/bcftools.git\n$ sudo yum install zlib-devel\n$ sudo yum install bzip2-devel\n$ sudo yum install xz-devel\n$ sudo yum install curl-devel\n$ cd bcftools\n$ make\n$ sudo make install\n$ cd ../htslib\n$ make\n$ sudo make install\n```\n\nThis should put `bgzip` and `tabix` into `/usr/local/bin`.\n\n### Compressing and indexing test intervals\n\nCompress and index the test interval file `sample.bed`, if not already done:\n\n```\n$ bgzip sample.bed\n$ tabix -p bed sample.bed.gz\n```\n\nThis creates two files: `sample.bed.gz` and `sample.bed.gz.tbi`.\n\nA test query would work like this:\n\n```\n$ tabix sample.bed.gz chr1:10000000-11000000\nchr1\t10037856      10038006\tid-501897\t102\nchr1\t10197056      10197206\tid-509857\t19 \n```\n\n### Node.js\n\nTo install Node.js:\n\n```\n$ sudo yum install epel-release\n$ sudo yum install nodejs\n$ sudo yum install npm\n```\n\n### Tabix server and client\n\nInstall the Node.js dependencies, if not installed:\n\n```\n$ cd tabix-service/server\n$ npm install\n$ cd ../client\n$ npm install\n```\n\n## Starting Tabix service\n\n```\n$ cd tabix-service/server\n$ export TABIX_SERVER_PORT=1234\n$ node app.js\n```\n\n## Starting Tabix test client\n\n```\n$ cd tabix-service/client\n$ export TABIX_CLIENT_PORT=4567\n$ node app.js\n```\n\nThen visit \u003ca href=\"http://localhost:4567\"\u003ehttp://localhost:4567\u003c/a\u003e to run test queries.\n\n![tabixservicesnapshot](https://cloud.githubusercontent.com/assets/33584/26523456/ca63436e-42cc-11e7-92ba-c2bedcc89812.png)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Falexpreynolds%2Ftabix-service","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Falexpreynolds%2Ftabix-service","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Falexpreynolds%2Ftabix-service/lists"}