{"id":17955503,"url":"https://github.com/heuermh/googlegenomics-api-provider-local-java","last_synced_at":"2025-04-03T16:49:23.929Z","repository":{"id":16574668,"uuid":"19328701","full_name":"heuermh/googlegenomics-api-provider-local-java","owner":"heuermh","description":"Implements the Google Genomics API locally, reading its data from local BAM files.","archived":false,"fork":false,"pushed_at":"2014-09-08T16:09:06.000Z","size":1062,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-02-09T05:37:57.855Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"Java","has_issues":false,"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/heuermh.png","metadata":{"files":{"readme":"README.rst","changelog":null,"contributing":"CONTRIBUTING.rst","funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2014-04-30T22:01:32.000Z","updated_at":"2016-05-25T17:27:17.000Z","dependencies_parsed_at":"2022-09-25T15:11:31.742Z","dependency_job_id":null,"html_url":"https://github.com/heuermh/googlegenomics-api-provider-local-java","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/heuermh%2Fgooglegenomics-api-provider-local-java","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/heuermh%2Fgooglegenomics-api-provider-local-java/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/heuermh%2Fgooglegenomics-api-provider-local-java/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/heuermh%2Fgooglegenomics-api-provider-local-java/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/heuermh","download_url":"https://codeload.github.com/heuermh/googlegenomics-api-provider-local-java/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":247043325,"owners_count":20874085,"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","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":"2024-10-29T10:28:54.282Z","updated_at":"2025-04-03T16:49:23.905Z","avatar_url":"https://github.com/heuermh.png","language":"Java","funding_links":[],"categories":[],"sub_categories":[],"readme":"api-provider-local-java  |Build Status|_\n==============================\n\n.. |Build Status| image:: https://travis-ci.org/googlegenomics/api-provider-local-java.png?branch=master\n.. _Build Status: https://travis-ci.org/googlegenomics/api-provider-local-java\n\n\nNote: this repo supports v0.1 of the GA4GH APIs. There is a different \n`python server \u003chttps://github.com/ga4gh/server\u003e`_ that will support v0.5 \nand will make this repo obsolete.\n\n.....\n\nGetting started  \n---------------\n\nTo use, first build the code using `Apache Maven \u003chttp://maven.apache.org/download.cgi\u003e`_::\n\n  cd api-provider-local-java\n  mvn package\n\nOnce built, use the jar file to start a local server::\n\n  java -cp target/api-provider-local-java-v1beta-jar-with-dependencies.jar com.google.cloud.genomics.localrepo.Server --dataset=testdata:testdata\n\nThere are two command line flags available:\n\n``--port=\u003cportnum\u003e``:\n  Sets the port that the server listens on for incoming connections. If\n  unspecified, the default is 5000.\n\n``--dataset=\u003cid\u003e:\u003cdirectory\u003e``:\n  This flag can occur zero or more times. With each instance of this flag, you\n  supply a dataset ID and a path to a directory on your local filesystem. When\n  the server is started, each directory is recursively traversed, and all ``.bam``\n  files with a corresponding sibling ``.bai`` file are included into the data\n  with the given dataset ID. For example, if you have the following directory\n  layout::\n\n    my_directory/\n      my_subdirectory/\n        foo.bam\n        foo.bam.bai\n      another_subdirectory/\n        bar.bam\n      baz.bam\n      baz.bam.bai\n\n  and you passed the flag ``--dataset=my_data:/path/to/my_directory``, then\n  ``my_directory/my_subdirectory/foo.bam`` and ``my_directory/baz.bam`` would be\n  included into a dataset with ID ``my_data``, but\n  ``my_directory/another_subdirectory/bar.bam`` would be excluded, due to not\n  having its sibling ``.bai`` file.\n\nGo to ``http://localhost:\u003cportnum\u003e/datasets`` to see your data.  \n\n\nProject status\n--------------\n\nThis repository has been replaced by the work on `ga4gh/server \u003chttp://github.com/ga4gh/server\u003e`_.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fheuermh%2Fgooglegenomics-api-provider-local-java","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fheuermh%2Fgooglegenomics-api-provider-local-java","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fheuermh%2Fgooglegenomics-api-provider-local-java/lists"}