{"action":"created","issue":{"url":"https://api.github.com/repos/Ensembl/VEP_plugins/issues/32","repository_url":"https://api.github.com/repos/Ensembl/VEP_plugins","labels_url":"https://api.github.com/repos/Ensembl/VEP_plugins/issues/32/labels{/name}","comments_url":"https://api.github.com/repos/Ensembl/VEP_plugins/issues/32/comments","events_url":"https://api.github.com/repos/Ensembl/VEP_plugins/issues/32/events","html_url":"https://github.com/Ensembl/VEP_plugins/issues/32","id":181358257,"number":32,"title":"missing dependency when downloading LoF plugin","user":{"login":"matthdsm","id":11850640,"avatar_url":"https://avatars.githubusercontent.com/u/11850640?v=3","gravatar_id":"","url":"https://api.github.com/users/matthdsm","html_url":"https://github.com/matthdsm","followers_url":"https://api.github.com/users/matthdsm/followers","following_url":"https://api.github.com/users/matthdsm/following{/other_user}","gists_url":"https://api.github.com/users/matthdsm/gists{/gist_id}","starred_url":"https://api.github.com/users/matthdsm/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/matthdsm/subscriptions","organizations_url":"https://api.github.com/users/matthdsm/orgs","repos_url":"https://api.github.com/users/matthdsm/repos","events_url":"https://api.github.com/users/matthdsm/events{/privacy}","received_events_url":"https://api.github.com/users/matthdsm/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2016-10-06T08:55:35Z","updated_at":"2016-10-06T10:46:47Z","closed_at":null,"body":"Hi,\r\n\r\nThe LofTee plugin has a missing dependency when downloading it with the automated installer.\r\ncurrent config is\r\n```\r\n    # LOFTEE\r\n    # Requires LoFtool_scores.txt file as first param (available in VEP_plugins GitHub repo)\r\n    {\r\n      \"key\" => \"LoF\",\r\n      \"helptip\" => \"LOFTEE identifies LoF (loss-of-function) variation\",\r\n      \"available\" => 0,\r\n      \"enabled\" => 0,\r\n      \"section\" => \"Pathogenicity predictions\",\r\n      \"plugin_url\" => \"https://raw.githubusercontent.com/konradjk/loftee/master/LoF.pm\",\r\n      \"requires_data\" => 1,\r\n      \"requires_install\" => 1,\r\n      \"params\" => [\r\n        \"@*\"\r\n      ]\r\n    },\r\n```\r\n\r\nBut the plugin depends on `splice_module.pl` which can be found in the same repo. Can this file be downloaded too when installing the loftee plugin?\r\n\r\nexcerpt from LoF.pm: \r\n```\r\npackage LoF;\r\nrequire \"splice_module.pl\";\r\n```\r\nI'm not familiar with the inner workings of the download process, but could something like this be added?\r\n\r\n```\r\n\"plugin_url\" => \"https://raw.githubusercontent.com/konradjk/loftee/master/LoF.pm\",\r\n\"plugin_depend_url\" => \"https://raw.githubusercontent.com/konradjk/loftee/master/splice_module.pl\",\r\n```\r\n\r\n\r\nThanks\r\nM\r\n"},"comment":{"url":"https://api.github.com/repos/Ensembl/VEP_plugins/issues/comments/251928239","html_url":"https://github.com/Ensembl/VEP_plugins/issues/32#issuecomment-251928239","issue_url":"https://api.github.com/repos/Ensembl/VEP_plugins/issues/32","id":251928239,"user":{"login":"willmclaren","id":1215653,"avatar_url":"https://avatars.githubusercontent.com/u/1215653?v=3","gravatar_id":"","url":"https://api.github.com/users/willmclaren","html_url":"https://github.com/willmclaren","followers_url":"https://api.github.com/users/willmclaren/followers","following_url":"https://api.github.com/users/willmclaren/following{/other_user}","gists_url":"https://api.github.com/users/willmclaren/gists{/gist_id}","starred_url":"https://api.github.com/users/willmclaren/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/willmclaren/subscriptions","organizations_url":"https://api.github.com/users/willmclaren/orgs","repos_url":"https://api.github.com/users/willmclaren/repos","events_url":"https://api.github.com/users/willmclaren/events{/privacy}","received_events_url":"https://api.github.com/users/willmclaren/received_events","type":"User","site_admin":false},"created_at":"2016-10-06T10:46:47Z","updated_at":"2016-10-06T10:46:47Z","body":"The plugin download system unfortunately isn't really an installer, that is why the script tells you further installation is required and that you should consult the plugin file to find out how to get it working:\r\n\r\n`` - This plugin requires installation\r\n`` - See [path]/LoF.pm for details\r\n\r\nBecause different plugins will have more or less complicated requirements than simply downloading another file, without using some more complex package system this is the best we can currently do."}}
{"actor":{"display_login":"willmclaren"}}