{"id":20765753,"url":"https://github.com/biopython/biopython_docker","last_synced_at":"2025-08-06T15:19:03.696Z","repository":{"id":29577865,"uuid":"33117528","full_name":"biopython/biopython_docker","owner":"biopython","description":"Dockerfiles to build Biopython instances","archived":false,"fork":false,"pushed_at":"2016-08-30T02:46:16.000Z","size":1170,"stargazers_count":28,"open_issues_count":1,"forks_count":10,"subscribers_count":14,"default_branch":"master","last_synced_at":"2025-04-30T10:02:43.257Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Shell","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/biopython.png","metadata":{"files":{"readme":"README.rst","changelog":null,"contributing":null,"funding":null,"license":"LICENSE.BSD-3-Clause","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2015-03-30T10:46:31.000Z","updated_at":"2024-05-03T10:11:44.000Z","dependencies_parsed_at":"2022-09-03T18:10:27.726Z","dependency_job_id":null,"html_url":"https://github.com/biopython/biopython_docker","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/biopython/biopython_docker","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biopython%2Fbiopython_docker","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biopython%2Fbiopython_docker/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biopython%2Fbiopython_docker/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biopython%2Fbiopython_docker/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/biopython","download_url":"https://codeload.github.com/biopython/biopython_docker/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biopython%2Fbiopython_docker/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":269102241,"owners_count":24360123,"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":"2025-08-06T02:00:09.910Z","response_time":99,"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":[],"created_at":"2024-11-17T11:18:43.286Z","updated_at":"2025-08-06T15:19:03.641Z","avatar_url":"https://github.com/biopython.png","language":"Shell","readme":"Docker containers for Biopython\n===============================\n\n.. image:: logo/logo_python_final.png\n   :scale: 40 %\n   :align: center\n\nHere you can find Docker containers that include Biopython.\n\nTo install these you will need Docker (https://www.docker.com/)\non Linux or Docker Toolbox (https://www.docker.com/products/docker-toolbox) on Windows/Mac.\n\nAll containers should include all dependencies which can be installed\nwithout licensing/copyright issues.\n\nThere are 5 containers available at this time:\n\n* A basic one where you ssh into to use it. No databases included.\n\n* A basic one where you ssh into to use it. With BioSQL.\n\n* One with a Jupyter (IPython Notebook) interface,\n\n* One with a Jupyter (IPython Notebook) interface including a Biopython\n  tutorial.\n\n* One for buildbot integration testing.\n\n\nFor each container there will be 2 versions: for Python 3 and legacy Python 2.\nFor now only Python 3 is available.\n\nInstallation and Usage\n======================\n\nBasic container\n---------------\n\nIn the basic container, you ssh into it and use it from there.\n\nPython 3::\n\n    docker pull biopython/biopython\n    docker run -t -i biopython/biopython /bin/bash\n    python3  # inside the container\n\nBioSQL container\n----------------\n\nPython 3::\n\n    docker pull biopython/biopython-sql\n    docker run -t -i biopython/biopython-sql /bin/bash\n    python3  # inside the container\n\nJupyter container\n-----------------\n\nHere you will need to point your browser to localhost:9803 (or 9802 on Python\n2).\n\n**If you are on boot2docker you need to do an extra port mapping step on your\nVM**\n\nPython 3::\n\n    docker pull biopython/biopython-notebook\n    docker run -p 9803:9803 -t -i biopython/biopython-notebook\n\nJupyter container with tutorials\n--------------------------------\n\nHere you will need to point your browser to localhost:9803 (or 9802 on Python\n2).\n\n**If you are on boot2docker you need to do an extra port mapping step on your\nVM**\n\nPython 3::\n\n    docker pull biopython/biopython-tutorial\n    docker run -p 9803:9803 -t -i biopython/biopython-tutorial\n\nMount your local directory to Docker (here are are naming it $PWD/scratch, but\nchange it as preferred)::\n\n    docker run -v $PWD:/scratch -e JUPYTER_UID=$UID -it -p 9803:9803 biopython-notebook\n\nBuildbot version\n================\n\n**You only need this if you help with our testing effort**\n\nYou will need to manually download the Docker file and update\n\nCHANGEUSER CHANGEPASS\n\nto your buildbot username and password\n\nPython 3::\n\n    #do this in an empty directory\n    wget https://raw.githubusercontent.com/biopython/biopython_docker/master/biopython-buildbot/Dockerfile\n    #REMEMBER TO CHANGE CHANGEUSER AND CHANGEPASS\n    docker build -t biopython-buildbot .\n    docker run -t -i biopython-buildbot\n\n\nLICENSING\n=========\n\nThe software herein is made available under a dual license under the\nBiopython historic license (see file LICENSE.Biopython) and the 3-clause\nBSD license (see file LICENSE.BSD-3-Clause)\n\nLogo credits and copyright: Vincent Davis\n\nAuthors: Tiago Antao and Tao Zhang with help from Björn Grüning\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbiopython%2Fbiopython_docker","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbiopython%2Fbiopython_docker","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbiopython%2Fbiopython_docker/lists"}