{"action":"created","issue":{"url":"https://api.github.com/repos/GMOD/Apollo/issues/1000","repository_url":"https://api.github.com/repos/GMOD/Apollo","labels_url":"https://api.github.com/repos/GMOD/Apollo/issues/1000/labels{/name}","comments_url":"https://api.github.com/repos/GMOD/Apollo/issues/1000/comments","events_url":"https://api.github.com/repos/GMOD/Apollo/issues/1000/events","html_url":"https://github.com/GMOD/Apollo/issues/1000","id":149861328,"number":1000,"title":"handleJbrowse does not seem to download plugins","user":{"login":"erasche","id":458683,"avatar_url":"https://avatars.githubusercontent.com/u/458683?v=3","gravatar_id":"","url":"https://api.github.com/users/erasche","html_url":"https://github.com/erasche","followers_url":"https://api.github.com/users/erasche/followers","following_url":"https://api.github.com/users/erasche/following{/other_user}","gists_url":"https://api.github.com/users/erasche/gists{/gist_id}","starred_url":"https://api.github.com/users/erasche/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/erasche/subscriptions","organizations_url":"https://api.github.com/users/erasche/orgs","repos_url":"https://api.github.com/users/erasche/repos","events_url":"https://api.github.com/users/erasche/events{/privacy}","received_events_url":"https://api.github.com/users/erasche/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/GMOD/Apollo/labels/bug","name":"bug","color":"fc2929"},{"url":"https://api.github.com/repos/GMOD/Apollo/labels/Workingon","name":"Workingon","color":"009800"}],"state":"open","locked":false,"assignee":{"login":"nathandunn","id":751274,"avatar_url":"https://avatars.githubusercontent.com/u/751274?v=3","gravatar_id":"","url":"https://api.github.com/users/nathandunn","html_url":"https://github.com/nathandunn","followers_url":"https://api.github.com/users/nathandunn/followers","following_url":"https://api.github.com/users/nathandunn/following{/other_user}","gists_url":"https://api.github.com/users/nathandunn/gists{/gist_id}","starred_url":"https://api.github.com/users/nathandunn/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nathandunn/subscriptions","organizations_url":"https://api.github.com/users/nathandunn/orgs","repos_url":"https://api.github.com/users/nathandunn/repos","events_url":"https://api.github.com/users/nathandunn/events{/privacy}","received_events_url":"https://api.github.com/users/nathandunn/received_events","type":"User","site_admin":false},"milestone":{"url":"https://api.github.com/repos/GMOD/Apollo/milestones/23","html_url":"https://github.com/GMOD/Apollo/milestones/2.0.3","labels_url":"https://api.github.com/repos/GMOD/Apollo/milestones/23/labels","id":1299980,"number":23,"title":"2.0.3","description":"Bugfixes and Chado re-implementation.\r\n\r\n- Closed issued: https://github.com/GMOD/Apollo/issues?q=is%3Apr+milestone%3A2.0.3+is%3Aclosed\r\n- Closed pull requests: https://github.com/GMOD/Apollo/pulls?q=is%3Apr+milestone%3A2.0.3+is%3Aclosed","creator":{"login":"nathandunn","id":751274,"avatar_url":"https://avatars.githubusercontent.com/u/751274?v=3","gravatar_id":"","url":"https://api.github.com/users/nathandunn","html_url":"https://github.com/nathandunn","followers_url":"https://api.github.com/users/nathandunn/followers","following_url":"https://api.github.com/users/nathandunn/following{/other_user}","gists_url":"https://api.github.com/users/nathandunn/gists{/gist_id}","starred_url":"https://api.github.com/users/nathandunn/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nathandunn/subscriptions","organizations_url":"https://api.github.com/users/nathandunn/orgs","repos_url":"https://api.github.com/users/nathandunn/repos","events_url":"https://api.github.com/users/nathandunn/events{/privacy}","received_events_url":"https://api.github.com/users/nathandunn/received_events","type":"User","site_admin":false},"open_issues":22,"closed_issues":74,"state":"open","created_at":"2015-09-10T19:58:08Z","updated_at":"2016-04-20T19:37:27Z","due_on":null,"closed_at":null},"comments":2,"created_at":"2016-04-20T19:20:02Z","updated_at":"2016-04-20T20:21:25Z","closed_at":null,"body":"```\r\n[hxr@leda:~/work/apollo]1$ gradle :installJBrowsePlugins                                                                                     (master) \r\n\r\n<snip>\r\n\r\n:evaluateJBrowseConfigs UP-TO-DATE\r\n:installJBrowse\r\ninstalling jbrowse [git:[url:https://github.com/GMOD/jbrowse, branch:master, alwaysPull:true, alwaysRecheck:true], plugins:[WebApollo:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true], GCContent:[git:https://github.com/cmdcolin/gccontent, branch:master, alwaysPull:true]]]\r\nusing bower to update: jbrowse-download\r\nbower jDataView#*           not-cached git://github.com/rbuels/jDataView.git#*\r\nbower jDataView#*              resolve git://github.com/rbuels/jDataView.git#*\r\n\r\n<snip>\r\n\r\nEvaluating plugin GCContent=[git:https://github.com/cmdcolin/gccontent, branch:master, alwaysPull:true]\r\nPlugin is supplied by git\r\nCloning 'https://github.com/cmdcolin/gccontent' into 'jbrowse-download/plugins/GCContent'\r\nusing bower to install: cmdcolin/gccontent#master\r\nbower gccontent#master      not-cached git://github.com/cmdcolin/gccontent.git#master\r\nbower gccontent#master         resolve git://github.com/cmdcolin/gccontent.git#master\r\nbower gccontent#master        checkout master\r\nbower gccontent#master        resolved git://github.com/cmdcolin/gccontent.git#7badc321e2\r\nbower gccontent#master         install gccontent#7badc321e2\r\n\r\ngccontent#7badc321e2 bower_components/gccontent\r\nBower dependencies already installed.  Type '/usr/local/bin/bower install -f allow-root' to force reinstallation of dependencies.\r\nInstalling Perl prerequisites ... done.\r\n\r\nFormatting Volvox example data ... done.\r\nTo see the volvox example data, browse to http://your.jbrowse.root/index.html?data=sample_data/json/volvox.\r\n\r\nFormatting Yeast example data ... done.\r\nTo see the yeast example data, browse to http://your.jbrowse.root/index.html?data=sample_data/json/yeast.\r\n\r\nBuilding and installing legacy wiggle format support (superseded by BigWig tracks) ... done.\r\n\r\nBuilding and installing legacy bam-to-json.pl support (superseded by direct BAM tracks) ... done.\r\nCLONED from https://github.com/cmdcolin/gccontent into jbrowse-download/plugins/GCContent\r\n\r\nBUILD SUCCESSFUL\r\n\r\nTotal time: 11.885 secs\r\n[hxr@leda:~/work/apollo]$                                                                                                                    (master) \r\n[hxr@leda:~/work/apollo]$ find . -iname 'gccontent'                                                                                          (master)\r\n[hxr@leda:~/work/apollo]$ ls jbrowse-download/plugins/GCContent                                                                             (master) \r\nls: klarte ikke å åpne jbrowse-download/plugins/GCContent: Fila eller mappa finnes ikke\r\n```\r\n\r\n\r\nIt says quite explicitly `CLONED from https://github.com/cmdcolin/gccontent into jbrowse-download/plugins/GCContent` except there's nothing there. (And given how JBrowse doesn't fail nicely when plugins are missing, this means JBrowse is non-functional in the apollo instance)"},"comment":{"url":"https://api.github.com/repos/GMOD/Apollo/issues/comments/212587630","html_url":"https://github.com/GMOD/Apollo/issues/1000#issuecomment-212587630","issue_url":"https://api.github.com/repos/GMOD/Apollo/issues/1000","id":212587630,"user":{"login":"erasche","id":458683,"avatar_url":"https://avatars.githubusercontent.com/u/458683?v=3","gravatar_id":"","url":"https://api.github.com/users/erasche","html_url":"https://github.com/erasche","followers_url":"https://api.github.com/users/erasche/followers","following_url":"https://api.github.com/users/erasche/following{/other_user}","gists_url":"https://api.github.com/users/erasche/gists{/gist_id}","starred_url":"https://api.github.com/users/erasche/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/erasche/subscriptions","organizations_url":"https://api.github.com/users/erasche/orgs","repos_url":"https://api.github.com/users/erasche/repos","events_url":"https://api.github.com/users/erasche/events{/privacy}","received_events_url":"https://api.github.com/users/erasche/received_events","type":"User","site_admin":false},"created_at":"2016-04-20T20:21:25Z","updated_at":"2016-04-20T20:21:25Z","body":"@nathandunn ok, great. I'm on a2d7fc0e76794e4e0c084a0344f967cdee7987f3.\r\n\r\nBtw you're spot on about bower_components getting wiped out. I `strace`d the process and noticed\r\n\r\n```\r\ndump.7533:rmdir(\"/home/hxr/work/apollo/bower_components/gccontent/css\") = 0\r\ndump.7533:rmdir(\"/home/hxr/work/apollo/bower_components/gccontent/js/Store/SeqFeature\") = 0\r\ndump.7533:rmdir(\"/home/hxr/work/apollo/bower_components/gccontent/js/Store\") = 0\r\ndump.7533:rmdir(\"/home/hxr/work/apollo/bower_components/gccontent/js/View/Track\") = 0\r\ndump.7533:rmdir(\"/home/hxr/work/apollo/bower_components/gccontent/js/View/Dialog\") = 0\r\ndump.7533:rmdir(\"/home/hxr/work/apollo/bower_components/gccontent/js/View\") = 0\r\ndump.7533:rmdir(\"/home/hxr/work/apollo/bower_components/gccontent/js\") = 0\r\ndump.7533:rmdir(\"/home/hxr/work/apollo/bower_components/gccontent/img\") = 0\r\ndump.7533:rmdir(\"/home/hxr/work/apollo/bower_components/gccontent\") = 0\r\ndump.7533:rmdir(\"/home/hxr/work/apollo/bower_components\") = 0\r\n```"}}