{"action":"created","issue":{"url":"https://api.github.com/repos/galaxyproject/tools-iuc/issues/714","repository_url":"https://api.github.com/repos/galaxyproject/tools-iuc","labels_url":"https://api.github.com/repos/galaxyproject/tools-iuc/issues/714/labels{/name}","comments_url":"https://api.github.com/repos/galaxyproject/tools-iuc/issues/714/comments","events_url":"https://api.github.com/repos/galaxyproject/tools-iuc/issues/714/events","html_url":"https://github.com/galaxyproject/tools-iuc/pull/714","id":146057254,"number":714,"title":"upgrade deseq2 and include tximport to use sailfish results directly ","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},"labels":[{"url":"https://api.github.com/repos/galaxyproject/tools-iuc/labels/wip","name":"wip","color":"fad8c7"}],"state":"open","locked":false,"assignee":null,"milestone":{"url":"https://api.github.com/repos/galaxyproject/tools-iuc/milestones/2","html_url":"https://github.com/galaxyproject/tools-iuc/milestones/BioConda%20Ready","labels_url":"https://api.github.com/repos/galaxyproject/tools-iuc/milestones/2/labels","id":1684353,"number":2,"title":"BioConda Ready","description":"Todo:\r\n - the tt_blacklist is empty\r\n - all tools are succesfully tested and deployed\r\n - the wiki/manual has been updated\r\n - Galaxy supports BioConda dependency resolution without manual configuration at the user side - this allows using dependencies that are bioconda-only and have no classical tool shed repository to fall back","creator":{"login":"yhoogstrate","id":2264697,"avatar_url":"https://avatars.githubusercontent.com/u/2264697?v=3","gravatar_id":"","url":"https://api.github.com/users/yhoogstrate","html_url":"https://github.com/yhoogstrate","followers_url":"https://api.github.com/users/yhoogstrate/followers","following_url":"https://api.github.com/users/yhoogstrate/following{/other_user}","gists_url":"https://api.github.com/users/yhoogstrate/gists{/gist_id}","starred_url":"https://api.github.com/users/yhoogstrate/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/yhoogstrate/subscriptions","organizations_url":"https://api.github.com/users/yhoogstrate/orgs","repos_url":"https://api.github.com/users/yhoogstrate/repos","events_url":"https://api.github.com/users/yhoogstrate/events{/privacy}","received_events_url":"https://api.github.com/users/yhoogstrate/received_events","type":"User","site_admin":false},"open_issues":8,"closed_issues":1,"state":"open","created_at":"2016-04-05T11:51:45Z","updated_at":"2016-04-18T13:03:01Z","due_on":null,"closed_at":null},"comments":23,"created_at":"2016-04-05T17:35:25Z","updated_at":"2016-04-18T16:53:26Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/galaxyproject/tools-iuc/pulls/714","html_url":"https://github.com/galaxyproject/tools-iuc/pull/714","diff_url":"https://github.com/galaxyproject/tools-iuc/pull/714.diff","patch_url":"https://github.com/galaxyproject/tools-iuc/pull/714.patch"},"body":"\r\n\r\nThis one is called DESeq2-TNG I should have named it RNA-seq TNG ;)\r\nI'm very excited about this PR and I'm seeking for help in testing. A little bit of background: until now we need to map the reads and use htseq-count to count reads in a region to feed this into DESeq2.\r\nOn the other hand Sailfish is a \"rapid Alignment-free Quantification of Isoform Abundance\" tool ... but we can not use the output natively with DESeq2. This has changed now!\r\n@mikelove has developed a nice tool called tximport that can read sailfish and salmon outputs directly and does the DESEq2 magic on top of it.\r\n\r\nThis PR updated our DESEq2 wrapper to make use of this new functionality. The workflow should be much simpler and much faster, as it is alignment free. I have created a new DESEq2 conda package to ease testing. So please activate the \"bgruening\" conda channel and run planemo on it if you want to provide feedback!\r\n\r\n@mikelove and me would love to have as much feedback as possible until the new bioc release in two weeks and the new DESeq2 release. After this there is a freeze for the next 6 month ... more or less.\r\n\r\nLet us know what you think we both are pretty excited about this :)\r\nCheers,\r\nMichael and Bjoern\r\n\r\nxref: https://github.com/galaxyproject/tools-iuc/pull/699\r\n"},"comment":{"url":"https://api.github.com/repos/galaxyproject/tools-iuc/issues/comments/211471396","html_url":"https://github.com/galaxyproject/tools-iuc/pull/714#issuecomment-211471396","issue_url":"https://api.github.com/repos/galaxyproject/tools-iuc/issues/714","id":211471396,"user":{"login":"mikelove","id":69203,"avatar_url":"https://avatars.githubusercontent.com/u/69203?v=3","gravatar_id":"","url":"https://api.github.com/users/mikelove","html_url":"https://github.com/mikelove","followers_url":"https://api.github.com/users/mikelove/followers","following_url":"https://api.github.com/users/mikelove/following{/other_user}","gists_url":"https://api.github.com/users/mikelove/gists{/gist_id}","starred_url":"https://api.github.com/users/mikelove/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mikelove/subscriptions","organizations_url":"https://api.github.com/users/mikelove/orgs","repos_url":"https://api.github.com/users/mikelove/repos","events_url":"https://api.github.com/users/mikelove/events{/privacy}","received_events_url":"https://api.github.com/users/mikelove/received_events","type":"User","site_admin":false},"created_at":"2016-04-18T16:53:25Z","updated_at":"2016-04-18T16:53:25Z","body":"Wow! I think that's actually an error at UCSC? The official symbol is SETD5:\r\n\r\nhttp://www.ncbi.nlm.nih.gov/gene/55209\r\n\r\nThe other values in the table are symbols.\r\n\r\nAm I seeing it wrong?"}}