{"action":"created","issue":{"url":"https://api.github.com/repos/galaxyproject/galaxy/issues/5496","repository_url":"https://api.github.com/repos/galaxyproject/galaxy","labels_url":"https://api.github.com/repos/galaxyproject/galaxy/issues/5496/labels{/name}","comments_url":"https://api.github.com/repos/galaxyproject/galaxy/issues/5496/comments","events_url":"https://api.github.com/repos/galaxyproject/galaxy/issues/5496/events","html_url":"https://github.com/galaxyproject/galaxy/issues/5496","id":295805744,"number":5496,"title":"failure to convert bam_native to bam","user":{"login":"wm75","id":4742081,"avatar_url":"https://avatars0.githubusercontent.com/u/4742081?v=4","gravatar_id":"","url":"https://api.github.com/users/wm75","html_url":"https://github.com/wm75","followers_url":"https://api.github.com/users/wm75/followers","following_url":"https://api.github.com/users/wm75/following{/other_user}","gists_url":"https://api.github.com/users/wm75/gists{/gist_id}","starred_url":"https://api.github.com/users/wm75/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/wm75/subscriptions","organizations_url":"https://api.github.com/users/wm75/orgs","repos_url":"https://api.github.com/users/wm75/repos","events_url":"https://api.github.com/users/wm75/events{/privacy}","received_events_url":"https://api.github.com/users/wm75/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":8,"created_at":"2018-02-09T09:30:05Z","updated_at":"2018-02-09T10:36:55Z","closed_at":null,"author_association":"CONTRIBUTOR","body":"I just started exploring the new bam_native datatype. I uploaded a bam file sorted by read names to the main server with its datatype declared as bam_native.\r\nNext, I tried to use the dataset (as bam) with `NGS: Samtools Sort` with the goal to produce a coordinate-sorted bam from it. What happened though is that the job paused as the original uploaded dataset was switched to an error state because the `CONVERTER_bam_native_to_bam` failed with\r\n```\r\nsort: invalid option -- '@'\r\nsort: invalid option -- 'O'\r\nsort: invalid option -- 'T'\r\nopen: No such file or directory\r\n[bam_sort_core] fail to open file 1\r\n```\r\nAs a weird side effect of this, the original dataset now appears twice in my history (once in green and once in red), but that's probably a different issue.\r\n\r\nSince this is a converter problem the same happens with any other tool that tries to use a bam_native dataset as bam, so currently bam_native datasets can only be used with tools that explicitly accept bam_native as input format."},"comment":{"url":"https://api.github.com/repos/galaxyproject/galaxy/issues/comments/364398082","html_url":"https://github.com/galaxyproject/galaxy/issues/5496#issuecomment-364398082","issue_url":"https://api.github.com/repos/galaxyproject/galaxy/issues/5496","id":364398082,"user":{"login":"mvdbeek","id":6804901,"avatar_url":"https://avatars1.githubusercontent.com/u/6804901?v=4","gravatar_id":"","url":"https://api.github.com/users/mvdbeek","html_url":"https://github.com/mvdbeek","followers_url":"https://api.github.com/users/mvdbeek/followers","following_url":"https://api.github.com/users/mvdbeek/following{/other_user}","gists_url":"https://api.github.com/users/mvdbeek/gists{/gist_id}","starred_url":"https://api.github.com/users/mvdbeek/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mvdbeek/subscriptions","organizations_url":"https://api.github.com/users/mvdbeek/orgs","repos_url":"https://api.github.com/users/mvdbeek/repos","events_url":"https://api.github.com/users/mvdbeek/events{/privacy}","received_events_url":"https://api.github.com/users/mvdbeek/received_events","type":"User","site_admin":false},"created_at":"2018-02-09T10:36:55Z","updated_at":"2018-02-09T10:36:55Z","author_association":"MEMBER","body":"> So would actually have to maintain two versions of the tool then - one for 18.01+ that uses a dedicated datatype, but isn't loaded in older instances, and a legacy tool that outputs bam?\r\n\r\nThat's the straightforward option, otherwise we could also deposit the datatype in a toolshed repo that you can refer to. TS datatypes will be ignored when a galaxy instance has a newer built-in datatype"}}
{"actor":{"display_login":"mvdbeek"}}