{"_id":"5735f181dc3e010e00827bb1","project":"5735936aafab441700723a50","parentDoc":null,"version":{"_id":"5735936aafab441700723a53","__v":12,"project":"5735936aafab441700723a50","createdAt":"2016-05-13T08:42:18.615Z","releaseDate":"2016-05-13T08:42:18.615Z","categories":["5735936aafab441700723a54","5735a32931a73b1700887c94","5735b55beceb872200abbc6c","5735b56eb667601700d3bd6f","5735b9ba4b0ab120000b7dd4","5735b9c94b0ab120000b7dd5","5735cb131f16241700c8a0f7","5735e5c4e4824c3400aa1f21","5735e5d9e4824c3400aa1f23","5735e5f2ec67f6290013ac72","573ecfe0804f901700a9dfc7","573f276c7eeb8b190094ca7d"],"is_deprecated":false,"is_hidden":false,"is_beta":false,"is_stable":false,"codename":"","version_clean":"1.0.0","version":"1.0"},"user":"573592b84b0ab120000b7d44","__v":3,"category":{"_id":"5735b9ba4b0ab120000b7dd4","project":"5735936aafab441700723a50","__v":0,"version":"5735936aafab441700723a53","sync":{"url":"","isSync":false},"reference":false,"createdAt":"2016-05-13T11:25:46.654Z","from_sync":false,"order":7,"slug":"configuration-options-1","title":"Configuration Options (Hosting)"},"updates":[],"next":{"pages":[],"description":""},"createdAt":"2016-05-13T15:23:45.570Z","link_external":false,"link_url":"","githubsync":"","sync_unique":"","hidden":false,"api":{"results":{"codes":[]},"settings":"","auth":"required","params":[],"url":""},"isReference":false,"order":2,"body":"```\n[REPOSITORIES]\n  ENSEMBL_URL = https://github.com/Ensembl\n  ENSEMBL_BRANCH = release/84\n\n  BIOPERL_URL = https://github.com/bioperl\n  BIOPERL_BRANCH = master\n\n  EG_METAZOA_PLUGIN_URL = https://github.com/EnsemblGenomes/eg-web-metazoa\n  EG_METAZOA_PLUGIN_BRANCH = release/eg/31\n  EG_METAZOA_PLUGIN_PACKAGE = EG::Metazoa\n\n  API_PLUGIN_URL = https://github.com/EnsemblGenomes/ensemblgenomes-api\n  API_PLUGIN_BRANCH = release/eg/31\n  API_PLUGIN_PACKAGE = EG::API\n\n  EG_COMMON_PLUGIN_URL = https://github.com/EnsemblGenomes/eg-web-common\n  EG_COMMON_PLUGIN_BRANCH = release/eg/31\n  EG_COMMON_PLUGIN_PACKAGE = EG::Common\n\n  PUBLIC_PLUGINS = [ ]\n```\nConnection/branch information for the Github repositories to be cloned\n- ``ENSEMBL_URL``/``ENSEMBL_BRANCH`` and ``BIOPERL_URL``/``BIOPERL_BRANCH`` are always required.  Several Ensel]mbl repositories are ``git clone``d from ``ENSEMBL_URL`` for both the Ensembl website and to support the import pipeline.\n- Additional plugins can be loaded from any public ``git`` repository by specifying ``<NAME>_PLUGIN_URL``, ``<NAME>_PLUGIN_BRANCH`` and ``<NAME>_PLUGIN_PACKAGE`` as above.  Plugins specified in this way will be added to ``ensembl-webcode/conf/Plugins.pm`` in the order they are listed in the ``.ini`` file so those at the top of the list will overwrite functions in plugins further down the list.\n- ``PUBLIC_PLUGINS`` can be loaded from the Ensembl ``public-plugins`` repository by specifying the directory and package name of each repository as in ``PUBLIC_PLUGINS = [ ensembl|EnsEMBL::Ensembl genoverse|EnsEMBL::Genoverse ]``\n[block:api-header]\n{\n  \"type\": \"basic\",\n  \"title\": \"Ensembl mirror setup\"\n}\n[/block]\n```\n[REPOSITORIES]\n  ENSEMBL_URL = https://github.com/Ensembl\n  ENSEMBL_BRANCH = release/84\n\n  BIOPERL_URL = https://github.com/bioperl\n  BIOPERL_BRANCH = master\n\n  PUBLIC_PLUGINS = [ ensembl|EnsEMBL::Ensembl ]\n```\n[block:api-header]\n{\n  \"type\": \"basic\",\n  \"title\": \"Lepbase setup\"\n}\n[/block]\n```\n[REPOSITORIES]\n  ENSEMBL_URL = https://github.com/Ensembl\n  ENSEMBL_BRANCH = release/84\n\n  SEARCH_PLUGIN_URL = https://github.com/lepbase/lepbase-search\n  SEARCH_PLUGIN_BRANCH = master\n  SEARCH_PLUGIN_PACKAGE = LepBase::Search\n\n  BLAST_PLUGIN_URL = https://github.com/lepbase/lepbase-blast-linkout\n  BLAST_PLUGIN_BRANCH = master\n  BLAST_PLUGIN_PACKAGE = LepBase::BLAST\n\n  BIOPERL_URL = https://github.com/bioperl\n  BIOPERL_BRANCH = master\n\n  LEPBASE_PLUGIN_URL = https://bitbucket.org/lepbase/lepbase-ensembl\n  LEPBASE_PLUGIN_BRANCH = develop\n  LEPBASE_PLUGIN_PACKAGE = EG::LepBase\n\n  API_PLUGIN_URL = https://github.com/EnsemblGenomes/ensemblgenomes-api\n  API_PLUGIN_BRANCH = release/eg/31\n  API_PLUGIN_PACKAGE = EG::API\n\n  EG_COMMON_PLUGIN_URL = https://github.com/EnsemblGenomes/eg-web-common\n  EG_COMMON_PLUGIN_BRANCH = release/eg/31\n  EG_COMMON_PLUGIN_PACKAGE = EG::Common\n\n  PUBLIC_PLUGINS = [ ]\n```","excerpt":"","slug":"repositories","type":"basic","title":"[REPOSITORIES]"}
``` [REPOSITORIES] ENSEMBL_URL = https://github.com/Ensembl ENSEMBL_BRANCH = release/84 BIOPERL_URL = https://github.com/bioperl BIOPERL_BRANCH = master EG_METAZOA_PLUGIN_URL = https://github.com/EnsemblGenomes/eg-web-metazoa EG_METAZOA_PLUGIN_BRANCH = release/eg/31 EG_METAZOA_PLUGIN_PACKAGE = EG::Metazoa API_PLUGIN_URL = https://github.com/EnsemblGenomes/ensemblgenomes-api API_PLUGIN_BRANCH = release/eg/31 API_PLUGIN_PACKAGE = EG::API EG_COMMON_PLUGIN_URL = https://github.com/EnsemblGenomes/eg-web-common EG_COMMON_PLUGIN_BRANCH = release/eg/31 EG_COMMON_PLUGIN_PACKAGE = EG::Common PUBLIC_PLUGINS = [ ] ``` Connection/branch information for the Github repositories to be cloned - ``ENSEMBL_URL``/``ENSEMBL_BRANCH`` and ``BIOPERL_URL``/``BIOPERL_BRANCH`` are always required. Several Ensel]mbl repositories are ``git clone``d from ``ENSEMBL_URL`` for both the Ensembl website and to support the import pipeline. - Additional plugins can be loaded from any public ``git`` repository by specifying ``<NAME>_PLUGIN_URL``, ``<NAME>_PLUGIN_BRANCH`` and ``<NAME>_PLUGIN_PACKAGE`` as above. Plugins specified in this way will be added to ``ensembl-webcode/conf/Plugins.pm`` in the order they are listed in the ``.ini`` file so those at the top of the list will overwrite functions in plugins further down the list. - ``PUBLIC_PLUGINS`` can be loaded from the Ensembl ``public-plugins`` repository by specifying the directory and package name of each repository as in ``PUBLIC_PLUGINS = [ ensembl|EnsEMBL::Ensembl genoverse|EnsEMBL::Genoverse ]`` [block:api-header] { "type": "basic", "title": "Ensembl mirror setup" } [/block] ``` [REPOSITORIES] ENSEMBL_URL = https://github.com/Ensembl ENSEMBL_BRANCH = release/84 BIOPERL_URL = https://github.com/bioperl BIOPERL_BRANCH = master PUBLIC_PLUGINS = [ ensembl|EnsEMBL::Ensembl ] ``` [block:api-header] { "type": "basic", "title": "Lepbase setup" } [/block] ``` [REPOSITORIES] ENSEMBL_URL = https://github.com/Ensembl ENSEMBL_BRANCH = release/84 SEARCH_PLUGIN_URL = https://github.com/lepbase/lepbase-search SEARCH_PLUGIN_BRANCH = master SEARCH_PLUGIN_PACKAGE = LepBase::Search BLAST_PLUGIN_URL = https://github.com/lepbase/lepbase-blast-linkout BLAST_PLUGIN_BRANCH = master BLAST_PLUGIN_PACKAGE = LepBase::BLAST BIOPERL_URL = https://github.com/bioperl BIOPERL_BRANCH = master LEPBASE_PLUGIN_URL = https://bitbucket.org/lepbase/lepbase-ensembl LEPBASE_PLUGIN_BRANCH = develop LEPBASE_PLUGIN_PACKAGE = EG::LepBase API_PLUGIN_URL = https://github.com/EnsemblGenomes/ensemblgenomes-api API_PLUGIN_BRANCH = release/eg/31 API_PLUGIN_PACKAGE = EG::API EG_COMMON_PLUGIN_URL = https://github.com/EnsemblGenomes/eg-web-common EG_COMMON_PLUGIN_BRANCH = release/eg/31 EG_COMMON_PLUGIN_PACKAGE = EG::Common PUBLIC_PLUGINS = [ ] ```