{"id":21662830,"url":"https://github.com/higlass/higlass-server","last_synced_at":"2025-04-11T23:42:27.995Z","repository":{"id":11928064,"uuid":"70836044","full_name":"higlass/higlass-server","owner":"higlass","description":"Server component for HiGlass that manages and serves tiled data","archived":false,"fork":false,"pushed_at":"2023-05-23T02:03:39.000Z","size":131016,"stargazers_count":19,"open_issues_count":55,"forks_count":21,"subscribers_count":17,"default_branch":"develop","last_synced_at":"2025-03-25T19:39:02.906Z","etag":null,"topics":["gehlenborglab","hi-c","higlass"],"latest_commit_sha":null,"homepage":"","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/higlass.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2016-10-13T18:28:20.000Z","updated_at":"2024-08-02T15:36:32.000Z","dependencies_parsed_at":"2022-09-02T07:41:12.149Z","dependency_job_id":null,"html_url":"https://github.com/higlass/higlass-server","commit_stats":null,"previous_names":[],"tags_count":102,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/higlass%2Fhiglass-server","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/higlass%2Fhiglass-server/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/higlass%2Fhiglass-server/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/higlass%2Fhiglass-server/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/higlass","download_url":"https://codeload.github.com/higlass/higlass-server/tar.gz/refs/heads/develop","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248497902,"owners_count":21113982,"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":["gehlenborglab","hi-c","higlass"],"created_at":"2024-11-25T10:18:17.468Z","updated_at":"2025-04-11T23:42:27.967Z","avatar_url":"https://github.com/higlass.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# HiGlass Server\n\nThe HiGlass Server supports [HiGlass](https://github.com/higlass/higlass) and [HiPiler](https://github.com/flekschas/hipiler)\nby providing APIs for accessing and uploading tiles generated by\n[Clodius](https://github.com/higlass/clodius).\n\n[![demo](https://img.shields.io/badge/higlass-👍-red.svg?colorB=0f5d92)](http://higlass.io)\n[![api](https://img.shields.io/badge/api-documentation-red.svg?colorB=0f5d92)](API.md)\n[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1308945.svg)](https://doi.org/10.5281/zenodo.1308945)\n\n\n_Note: that the HiGlass Server itself only provides an API, and does not serve any HTML._\n\n## Installation\n\n**Prerequirements**:\n\n- Python `\u003e=v3.6`\n\n### Docker\n\nThe easiest way to run HiGlass with HiGlass Server is with Docker. More information is available at [higlass-docker](https://github.com/higlass/higlass-docker#readme) or check out the [Dockerfile](docker-context/Dockerfile).\n\nThis project also includes a Dockerfile in the docker-context directory that can be used to run a locally checked out copy of higlass-server as follows:\n```bash\ndocker build -t higlass-server -f docker-context/Dockerfile .\ndocker run -d --cap-add SYS_ADMIN --device /dev/fuse --security-opt apparmor:unconfined --name higlass-server higlass-server\n```\n\n### Manually\n\nTo install HiGlass Server manually follow the steps below. Note we strongly recommend to create a virtual environment using [Virtualenvwrapper](https://pypi.python.org/pypi/virtualenvwrapper) for example. Skip step 2 if you don't work with virtual environments.\n\n```bash\ngit clone https://github.com/higlass/higlass-server \u0026\u0026 cd higlass-server\n```\n\n#### Manually with virtualenvwrapper\n\n```bash\nmkvirtualenv -a $(pwd) -p $(which python3) higlass-server \u0026\u0026 workon higlass-server\npip install --upgrade -r ./requirements.txt\npython manage.py migrate\npython manage.py runserver\n```\n\n#### Manually with conda\n\n```bash\nconda env create -f environment.yml\nconda activate higlass-server\npython manage.py migrate\npython manage.py runserver\n```\n\nTo enable the register_url api endpoint, HiGlass depends on a project called httpfs to cache external url files. Tests depend on this process running. Set it up as follows:\n```bash\npip install simple-httpfs\n\nmkdir -p media/http\nmkdir -p media/https\nsimple-httpfs media/http\nsimple-httpfs media/https\n```\n\nOr simply use `./unit_tests.sh`.\n\n---\n\n## Uploading Files\n\nAlthough there is an API endpoint for uploading files, but it is more direct to use a `manage.py` script:\n```\nCOOLER=dixon2012-h1hesc-hindiii-allreps-filtered.1000kb.multires.cool\nHITILE=wgEncodeCaltechRnaSeqHuvecR1x75dTh1014IlnaPlusSignalRep2.hitile\n\nwget -P data/ https://s3.amazonaws.com/pkerp/public/$COOLER\nwget -P data/ https://s3.amazonaws.com/pkerp/public/$HITILE\n\npython manage.py ingest_tileset --filename data/$COOLER --filetype cooler --datatype matrix --uid cooler-demo\npython manage.py ingest_tileset --filename data/$HITILE --filetype hitile --datatype vector --uid hitile-demo\n```\n\nWe can now use the API to get information about a tileset, or to get the tile data itself:\n```\ncurl http://localhost:8000/api/v1/tileset_info/?d=hitile-demo\ncurl http://localhost:8000/api/v1/tiles/?d=hitile-demo.0.0.0\n```\n\n---\n\n## Development\n\n**Start** the server:\n\n```\npython manage.py runserver localhost:8001\n// or\nnpm start\n```\n\n**Test** the server:\n\n```\n./test.sh\n// or\nnpm test\n```\n\n**Bump version** of server:\n\n```\nbumpversion patch\n```\n\n**Update** source code:\n\n```\n./update.sh\n```\n\n## Troubleshooting\n\n**pybbi installation fails on macOS**: Check out https://github.com/nvictus/pybbi/issues/2\n\n### macOS 10.15 dependencies\n\n- `brew install hdf5`\n- `brew install libpng`\n- `brew install jpeg`\n- [FUSE for Mac](https://osxfuse.github.io/)\n\n\n## License\n\nThe code in this repository is provided under the MIT License.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fhiglass%2Fhiglass-server","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fhiglass%2Fhiglass-server","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fhiglass%2Fhiglass-server/lists"}