{"action":"created","issue":{"url":"https://api.github.com/repos/ODoSE/odose.nl/issues/3","labels_url":"https://api.github.com/repos/ODoSE/odose.nl/issues/3/labels{/name}","comments_url":"https://api.github.com/repos/ODoSE/odose.nl/issues/3/comments","events_url":"https://api.github.com/repos/ODoSE/odose.nl/issues/3/events","html_url":"https://github.com/ODoSE/odose.nl/issues/3","id":114089874,"number":3,"title":"Workflow with external genomes","user":{"login":"chatcrawler","id":2347378,"avatar_url":"https://avatars.githubusercontent.com/u/2347378?v=3","gravatar_id":"","url":"https://api.github.com/users/chatcrawler","html_url":"https://github.com/chatcrawler","followers_url":"https://api.github.com/users/chatcrawler/followers","following_url":"https://api.github.com/users/chatcrawler/following{/other_user}","gists_url":"https://api.github.com/users/chatcrawler/gists{/gist_id}","starred_url":"https://api.github.com/users/chatcrawler/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/chatcrawler/subscriptions","organizations_url":"https://api.github.com/users/chatcrawler/orgs","repos_url":"https://api.github.com/users/chatcrawler/repos","events_url":"https://api.github.com/users/chatcrawler/events{/privacy}","received_events_url":"https://api.github.com/users/chatcrawler/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":{"login":"timtebeek","id":1027334,"avatar_url":"https://avatars.githubusercontent.com/u/1027334?v=3","gravatar_id":"","url":"https://api.github.com/users/timtebeek","html_url":"https://github.com/timtebeek","followers_url":"https://api.github.com/users/timtebeek/followers","following_url":"https://api.github.com/users/timtebeek/following{/other_user}","gists_url":"https://api.github.com/users/timtebeek/gists{/gist_id}","starred_url":"https://api.github.com/users/timtebeek/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/timtebeek/subscriptions","organizations_url":"https://api.github.com/users/timtebeek/orgs","repos_url":"https://api.github.com/users/timtebeek/repos","events_url":"https://api.github.com/users/timtebeek/events{/privacy}","received_events_url":"https://api.github.com/users/timtebeek/received_events","type":"User","site_admin":false},"milestone":null,"comments":1,"created_at":"2015-10-29T16:31:06Z","updated_at":"2015-10-29T18:51:16Z","closed_at":null,"body":"Hi Tim.\r\n\r\nIt seems that I cannot finish any analyses based solely on external genomes with ODoSE (correct me where I am wrong), and I think this is mainly due to the fact that one cannot select any published GenBank genomes in ODoSE anymore.\r\n\r\nMore specifically: when I upload all my external genomes in nucleotide *fasta-file-format (as described in the main publication; Vos et al. 2013 PLoS ONE), I don't find a way to select these and translate their genes into amino acid sequences prior to the orthoMCL step (which is based on protein-BLAST searches, blastp).\r\n\r\nHowever, when I opt to upload amino acid *fasta-files in the first place, I also get stuck, this time right AFTER the orthoMCL step. The latter runs through efficiently, but in order to execute the \"Extract & categorize orthologs from OrthoMCL groups file\" step I would have to choose *GenBank Project IDs* which were not created in the first place (in the absence of selectable gbk-files). And thus the whole analysis lead to nonsensical output, e.g., no SICOs are reported and there are as many genomes as genes declared in the output.\r\n\r\nFor the moment I don't see a way out of this, please let me know, what you would suggest me to do.\r\n\r\nCheers\r\n\r\nSéb\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/ODoSE/odose.nl/issues/comments/152285312","html_url":"https://github.com/ODoSE/odose.nl/issues/3#issuecomment-152285312","issue_url":"https://api.github.com/repos/ODoSE/odose.nl/issues/3","id":152285312,"user":{"login":"timtebeek","id":1027334,"avatar_url":"https://avatars.githubusercontent.com/u/1027334?v=3","gravatar_id":"","url":"https://api.github.com/users/timtebeek","html_url":"https://github.com/timtebeek","followers_url":"https://api.github.com/users/timtebeek/followers","following_url":"https://api.github.com/users/timtebeek/following{/other_user}","gists_url":"https://api.github.com/users/timtebeek/gists{/gist_id}","starred_url":"https://api.github.com/users/timtebeek/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/timtebeek/subscriptions","organizations_url":"https://api.github.com/users/timtebeek/orgs","repos_url":"https://api.github.com/users/timtebeek/repos","events_url":"https://api.github.com/users/timtebeek/events{/privacy}","received_events_url":"https://api.github.com/users/timtebeek/received_events","type":"User","site_admin":false},"created_at":"2015-10-29T18:51:16Z","updated_at":"2015-10-29T18:51:16Z","body":"Hi @chatcrawler ,\r\nAllow me to copy what I also sent in an email earlier, in hopes that it helps, or at least helps pinpoint the exact problem:\r\n> The functionality [to run external genomes] is still there! It's just switched around a bit since the Galaxy devs broke the old way of side-loading external genomes. The manual still needs to be posted to the website, but here's the gist:\r\n- Start a new history\r\n- Drag (DNA) fasta files into your history, or upload using the Icon top left, or with `Get Data > Upload File`. Be sure to set the type/extension to fasta when you do.\r\n- Select the tool `Ortholog Direction of Selection Engine > Upload genomes`\r\n- For each of your uploaded fasta files, provide a short (<10) unique label.\r\n- Execute the tool once you've added all external genomes, this should result in a single new history item.\r\n- At workflow `Step 2: Extract & translate genes`, select your new history item of externally uploaded genomes\r\n- Continue as before."}}