{"id":33257970,"url":"https://github.com/biopython/galaxy_packages","last_synced_at":"2025-11-21T20:02:54.879Z","repository":{"id":10578963,"uuid":"12787339","full_name":"biopython/galaxy_packages","owner":"biopython","description":"Biopython package definitions for the Galaxy Tool Shed (OBSOLETE)","archived":true,"fork":false,"pushed_at":"2017-04-11T16:40:15.000Z","size":22,"stargazers_count":8,"open_issues_count":0,"forks_count":2,"subscribers_count":5,"default_branch":"master","last_synced_at":"2025-09-09T16:38:21.799Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"http://toolshed.g2.bx.psu.edu/view/biopython/","language":null,"has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"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":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2013-09-12T15:31:57.000Z","updated_at":"2025-01-22T13:44:31.000Z","dependencies_parsed_at":"2022-09-22T14:28:56.154Z","dependency_job_id":null,"html_url":"https://github.com/biopython/galaxy_packages","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/biopython/galaxy_packages","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biopython%2Fgalaxy_packages","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biopython%2Fgalaxy_packages/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biopython%2Fgalaxy_packages/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biopython%2Fgalaxy_packages/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/biopython","download_url":"https://codeload.github.com/biopython/galaxy_packages/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biopython%2Fgalaxy_packages/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":285681625,"owners_count":27213755,"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":"2025-11-21T02:00:06.175Z","response_time":61,"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":"2025-11-17T03:00:25.165Z","updated_at":"2025-11-21T20:02:54.874Z","avatar_url":"https://github.com/biopython.png","language":null,"funding_links":[],"categories":["Awesome Galaxy"],"sub_categories":["Tools"],"readme":"Biopython package definitions for the Galaxy Tool Shed (OBSOLETE)\n=================================================================\n\nFor an introduction to the Biopython Project, please see\nhttp://biopython.org - and for an introduction to the\nGalaxy Project, please see http://galaxyproject.org/\n\nThe Galaxy web platform is extensible allowing addition of\nnew tools to a Galaxy instance. These tools are shared via\na Galaxy Tool Shed, primarily http://toolshed.g2.bx.psu.edu\nand the Test Tool Shed http://testtoolshed.g2.bx.psu.edu\n\nIn addition to new tools, the Galaxy Tool Shed also included\nsoftware package definitions for use as dependencies. This\nrepository was for the development of the Biopython package\ndefinitions shared on the main Tool Shed and Test Tool Shed:\n\n* http://toolshed.g2.bx.psu.edu/view/biopython/\n* http://testtoolshed.g2.bx.psu.edu/view/biopython/\n\nNote that each release of Biopython gets its own predicatably\nnamed entry on the Tool Shed, so that tools using Biopython\ncan specify the exact version of Biopython required. This is\nimportant for reproducibility which is a Galaxy design goal.\n\nHowever, since 2017 the Galaxy community has moved away from\nthis home-grown dependency system and adopted Conda, and\nin particular the BioConda channel. This covers Biopython:\n\n- https://anaconda.org/bioconda/biopython\n- https://bioconda.github.io/recipes/biopython/README.html\n- https://github.com/bioconda/bioconda-recipes/tree/master/recipes/biopython\n\nInstructions for Galaxy Tool Authors\n====================================\n\nIf you are writing a Galaxy Tool which uses a Python script\ndependent on Biopython, in order for the Galaxy Tool Shed to\nautomatically install Biopython you must include a\n``tool_dependencies.xml`` file declaring this as a\ndependency, e.g.::\n\n  \u003c?xml version=\"1.0\"?\u003e\n  \u003crepositories description=\"Requires Biopython as a dependency.\"\u003e\n    \u003crepository name=\"package_biopython_1_65\" owner=\"biopython\" /\u003e\n  \u003c/repositories\u003e\n\nAlso, in your tool XML file(s) you must include::\n\n  \u003crequirements\u003e\n    \u003crequirement type=\"package\" version=\"1.65\"\u003ebiopython\u003c/requirement\u003e\n  \u003c/requirements\u003e\n\nThis will work on the main Tool Shed or the Test Tool Shed where\nit will refer to these packages:\n\n* http://toolshed.g2.bx.psu.edu/view/biopython/package_biopython_1_65\n* http://testtoolshed.g2.bx.psu.edu/view/biopython/package_biopython_1_65\n\nHere is an example declaring a dependency on Biopython this way:\n\n* https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans\n* http://toolshed.g2.bx.psu.edu/view/peterjc/align_back_trans\n* http://testtoolshed.g2.bx.psu.edu/view/peterjc/align_back_trans\n\nNote since it is a compile time requirement, the Biopython package\nitself will depend on NumPy, so you do not need to also declare\nthat as an explicit dependency.\n\nHowever, the package will not trigger the installation of optional\npackages such as ReportLab, MatPlotLib or NetworkX which parts of\nBiopython require.\n\nSo, if for example you are writing a Galaxy tool in Python using\nBiopython, MatPlotLib and SciPy you must explicitly declare them all\nas dependencies in your ``repository_dependencies.xml`` file, e.g.::\n\n  \u003c?xml version=\"1.0\"?\u003e\n  \u003crepositories description=\"Requires Biopython, MatPlotLib and SciPy.\"\u003e\n    \u003crepository name=\"package_biopython_1_65\" owner=\"biopython\" /\u003e\n    \u003crepository name=\"package_matplotlib_1_2\" owner=\"iuc\" /\u003e\n    \u003crepository name=\"package_scipy_0_14\" owner=\"iuc\" /\u003e\n  \u003c/repositories\u003e\n\nAnd in your tool XML file(s) you would include::\n\n  \u003crequirements\u003e\n    \u003crequirement type=\"package\" version=\"1.65\"\u003ebiopython\u003c/requirement\u003e\n    \u003crequirement type=\"package\" version=\"1.4\"\u003ematplotlib\u003c/requirement\u003e\n    \u003crequirement type=\"package\" version=\"0.14\"\u003escipy\u003c/requirement\u003e\n  \u003c/requirements\u003e\n\nThis will work on the main Tool Shed refering to these packages\n(and similarly on the Test Tool Shed):\n\n* http://toolshed.g2.bx.psu.edu/view/biopython/package_biopython_1_65\n* http://toolshed.g2.bx.psu.edu/view/iuc/package_matplotlib_1_4\n* http://toolshed.g2.bx.psu.edu/view/iuc/package_scipy_0_14\n\nThese additional dependencies are maintained by the IUC, or in full\nthe \"Intergalactic Utilities Commission\" which is the tongue-in-cheek\nname of the Galaxy Tool Shed review team, see:\nhttp://wiki.galaxyproject.org/ReviewingToolShedRepositories\n\nWhen looking for how to add further dependencies, search the Tool Shed\nfor \"Tool dependency definitions\", and in particular look for those\nfrom the IUC:\n\n* http://toolshed.g2.bx.psu.edu/view/iuc/\n* http://testtoolshed.g2.bx.psu.edu/view/iuc/\n\nIn addition to the examples above, the following are of particular\nrelevance:\n\n* https://testtoolshed.g2.bx.psu.edu/view/iuc/package_python_reportlab_3_1_44\n* https://testtoolshed.g2.bx.psu.edu/view/iuc/package_networkx_1_9\n\nFor full details on how to define dependencies on the Galaxy Tool Shed,\nsee http://wiki.galaxyproject.org/DefiningRepositoryDependencies\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbiopython%2Fgalaxy_packages","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbiopython%2Fgalaxy_packages","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbiopython%2Fgalaxy_packages/lists"}