{"action":"created","issue":{"url":"https://api.github.com/repos/Ecogenomics/CheckM/issues/34","labels_url":"https://api.github.com/repos/Ecogenomics/CheckM/issues/34/labels{/name}","comments_url":"https://api.github.com/repos/Ecogenomics/CheckM/issues/34/comments","events_url":"https://api.github.com/repos/Ecogenomics/CheckM/issues/34/events","html_url":"https://github.com/Ecogenomics/CheckM/issues/34","id":94062559,"number":34,"title":"Continue/Update Option","user":{"login":"hunter-cameron","id":6765020,"avatar_url":"https://avatars.githubusercontent.com/u/6765020?v=3","gravatar_id":"","url":"https://api.github.com/users/hunter-cameron","html_url":"https://github.com/hunter-cameron","followers_url":"https://api.github.com/users/hunter-cameron/followers","following_url":"https://api.github.com/users/hunter-cameron/following{/other_user}","gists_url":"https://api.github.com/users/hunter-cameron/gists{/gist_id}","starred_url":"https://api.github.com/users/hunter-cameron/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/hunter-cameron/subscriptions","organizations_url":"https://api.github.com/users/hunter-cameron/orgs","repos_url":"https://api.github.com/users/hunter-cameron/repos","events_url":"https://api.github.com/users/hunter-cameron/events{/privacy}","received_events_url":"https://api.github.com/users/hunter-cameron/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":3,"created_at":"2015-07-09T14:21:45Z","updated_at":"2015-07-15T21:21:31Z","closed_at":"2015-07-15T21:21:31Z","body":"I think it would be useful to have a feature (probably as a command line option) to allow users to add new genomes to the genome bins directory of past CheckM analyses and then rerun CheckM in \"update\" mode where only the new files are processed and all output files are updated to reflect the additions.\r\n\r\nWe have a continually growing database of several hundred bacterial genomes that we like to keep up-to-date CheckM analyses for and it consumes a fair bit of unnecessary computation time to run the full analysis over when we add a few new genomes. "},"comment":{"url":"https://api.github.com/repos/Ecogenomics/CheckM/issues/comments/121753102","html_url":"https://github.com/Ecogenomics/CheckM/issues/34#issuecomment-121753102","issue_url":"https://api.github.com/repos/Ecogenomics/CheckM/issues/34","id":121753102,"user":{"login":"dparks1134","id":3688336,"avatar_url":"https://avatars.githubusercontent.com/u/3688336?v=3","gravatar_id":"","url":"https://api.github.com/users/dparks1134","html_url":"https://github.com/dparks1134","followers_url":"https://api.github.com/users/dparks1134/followers","following_url":"https://api.github.com/users/dparks1134/following{/other_user}","gists_url":"https://api.github.com/users/dparks1134/gists{/gist_id}","starred_url":"https://api.github.com/users/dparks1134/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dparks1134/subscriptions","organizations_url":"https://api.github.com/users/dparks1134/orgs","repos_url":"https://api.github.com/users/dparks1134/repos","events_url":"https://api.github.com/users/dparks1134/events{/privacy}","received_events_url":"https://api.github.com/users/dparks1134/received_events","type":"User","site_admin":false},"created_at":"2015-07-15T21:21:31Z","updated_at":"2015-07-15T21:21:31Z","body":"No, it will not update the processed genomes so you have results for 101. Actually, the *lineage_wf* command will refuse to run if you provide it with an existing directory so previous results are not overwritten. \r\n\r\nI agree some sort of *update* command would be useful, but this is unlikely to happen in the short term. I suggest just processing new genomes to a new output directory. This wouldn't help with generating plots, but it is easy enough to concatenate tables together."}}