{"action":"created","issue":{"url":"https://api.github.com/repos/galaxyproject/galaxy/issues/476","labels_url":"https://api.github.com/repos/galaxyproject/galaxy/issues/476/labels{/name}","comments_url":"https://api.github.com/repos/galaxyproject/galaxy/issues/476/comments","events_url":"https://api.github.com/repos/galaxyproject/galaxy/issues/476/events","html_url":"https://github.com/galaxyproject/galaxy/pull/476","id":95698910,"number":476,"title":"[15.05] Disable extra BAM file metadata for now.","user":{"login":"jmchilton","id":216771,"avatar_url":"https://avatars.githubusercontent.com/u/216771?v=3","gravatar_id":"","url":"https://api.github.com/users/jmchilton","html_url":"https://github.com/jmchilton","followers_url":"https://api.github.com/users/jmchilton/followers","following_url":"https://api.github.com/users/jmchilton/following{/other_user}","gists_url":"https://api.github.com/users/jmchilton/gists{/gist_id}","starred_url":"https://api.github.com/users/jmchilton/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jmchilton/subscriptions","organizations_url":"https://api.github.com/users/jmchilton/orgs","repos_url":"https://api.github.com/users/jmchilton/repos","events_url":"https://api.github.com/users/jmchilton/events{/privacy}","received_events_url":"https://api.github.com/users/jmchilton/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":12,"created_at":"2015-07-17T16:59:18Z","updated_at":"2015-07-20T22:31:57Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/galaxyproject/galaxy/pulls/476","html_url":"https://github.com/galaxyproject/galaxy/pull/476","diff_url":"https://github.com/galaxyproject/galaxy/pull/476.diff","patch_url":"https://github.com/galaxyproject/galaxy/pull/476.patch"},"body":"I think this needs to be disabled until pysam egg is updated. This extra collection crashes Galaxy server processes when unsorted bam files are indexed using retry metadata internally, it breaks applications that previously worked with extrenal metadata, and causes at least one automated test to fail.\r\n\r\n```\r\n./run_tests.sh -framework -id compare_bam_as_sam\r\n```"},"comment":{"url":"https://api.github.com/repos/galaxyproject/galaxy/issues/comments/123073801","html_url":"https://github.com/galaxyproject/galaxy/pull/476#issuecomment-123073801","issue_url":"https://api.github.com/repos/galaxyproject/galaxy/issues/476","id":123073801,"user":{"login":"bgruening","id":469983,"avatar_url":"https://avatars.githubusercontent.com/u/469983?v=3","gravatar_id":"","url":"https://api.github.com/users/bgruening","html_url":"https://github.com/bgruening","followers_url":"https://api.github.com/users/bgruening/followers","following_url":"https://api.github.com/users/bgruening/following{/other_user}","gists_url":"https://api.github.com/users/bgruening/gists{/gist_id}","starred_url":"https://api.github.com/users/bgruening/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bgruening/subscriptions","organizations_url":"https://api.github.com/users/bgruening/orgs","repos_url":"https://api.github.com/users/bgruening/repos","events_url":"https://api.github.com/users/bgruening/events{/privacy}","received_events_url":"https://api.github.com/users/bgruening/received_events","type":"User","site_admin":false},"created_at":"2015-07-20T22:31:56Z","updated_at":"2015-07-20T22:31:56Z","body":"I completely got rid of the egg and removed the metadata part, manually.\r\nI now have a recent pysam egg in my virtualenv but without your changes. Nothing we can use for other :( sorry."}}