{"id":13704802,"url":"https://github.com/LooseLab/bulkVis","last_synced_at":"2025-05-05T12:32:12.851Z","repository":{"id":49894022,"uuid":"118934630","full_name":"LooseLab/bulkvis","owner":"LooseLab","description":null,"archived":false,"fork":false,"pushed_at":"2024-11-07T14:47:37.000Z","size":1422,"stargazers_count":46,"open_issues_count":20,"forks_count":9,"subscribers_count":6,"default_branch":"2.0","last_synced_at":"2024-11-07T15:43:57.559Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Python","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/LooseLab.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}},"created_at":"2018-01-25T15:59:31.000Z","updated_at":"2024-11-07T14:47:49.000Z","dependencies_parsed_at":"2022-08-25T18:40:21.834Z","dependency_job_id":"c1a795e0-71ef-45b6-abb2-e2ef022ca473","html_url":"https://github.com/LooseLab/bulkvis","commit_stats":null,"previous_names":[],"tags_count":3,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LooseLab%2Fbulkvis","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LooseLab%2Fbulkvis/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LooseLab%2Fbulkvis/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LooseLab%2Fbulkvis/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/LooseLab","download_url":"https://codeload.github.com/LooseLab/bulkvis/tar.gz/refs/heads/2.0","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":252497602,"owners_count":21757645,"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":"2024-08-02T22:00:17.422Z","updated_at":"2025-05-05T12:32:12.510Z","avatar_url":"https://github.com/LooseLab.png","language":"Python","readme":"⇜ bulkvis ⇝\n============\n\nAn app written in Python3 using [Bokeh][1] to visualise raw squiggle data from Oxford Nanopore Technologies (ONT) bulkfiles. \n\nQuickstart\n==========\n\nOur preferred installation method uses `conda` with this environment setup:\n```yaml\nname: bulkvis\nchannels:\n  - bioconda\n  - conda-forge\n  - defaults\ndependencies:\n  - python=3.11\n  - pip\n  - pip:\n    - numpy==1.26.4\n    - git+https://github.com/LooseLab/bulkvis.git@2.0\n```\n\nEither copy the YAML above into a file or:\n\n```console\ncurl -O https://raw.githubusercontent.com/LooseLab/bulkvis/2.0/env.yml\nconda env create -f env.yml\n```\n\nThen bulkvis can be started using:\n```console\nconda activate bulkvis\nbulkvis serve \u003cBULK_FILE_DIRECTORY\u003e --show\n```\n\n\u003cdetails\u003e\n\u003csummary\u003eor with another python source\u003c/summary\u003e\n\n```bash\n# Make a python3 virtual environment\npython3 -m venv bulkvis\n\n# Activate virtual environment\nsource bulkvis/bin/activate\n\n# Clone the repo to your installation/projects directory\npip install git+https://github.com/LooseLab/bulkvis.git@2.0\n\n# Start bokeh server\nbulkvis serve \u003cBULK_FILE_DIRECTORY\u003e --show\n```\n\u003c/details\u003e\n\nOther install requires:\n===\n\nTo open some bulk FAST5 files [`vbz compression plugins`][2] are required. \nThese are written and maintained by Oxford Nanopore Technologies.\n\n\n [1]: https://github.com/bokeh/bokeh/\n [2]: https://github.com/nanoporetech/vbz_compression\n","funding_links":[],"categories":["Long-read Sequencing Tools"],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FLooseLab%2FbulkVis","html_url":"https://awesome.ecosyste.ms/projects/github.com%2FLooseLab%2FbulkVis","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FLooseLab%2FbulkVis/lists"}