{"action":"created","issue":{"url":"https://api.github.com/repos/BD2KGenomics/cgl-docker-lib/issues/76","labels_url":"https://api.github.com/repos/BD2KGenomics/cgl-docker-lib/issues/76/labels{/name}","comments_url":"https://api.github.com/repos/BD2KGenomics/cgl-docker-lib/issues/76/comments","events_url":"https://api.github.com/repos/BD2KGenomics/cgl-docker-lib/issues/76/events","html_url":"https://github.com/BD2KGenomics/cgl-docker-lib/pull/76","id":128376518,"number":76,"title":"Use bwa-kit for alt aware alignment","user":{"login":"fnothaft","id":3752466,"avatar_url":"https://avatars.githubusercontent.com/u/3752466?v=3","gravatar_id":"","url":"https://api.github.com/users/fnothaft","html_url":"https://github.com/fnothaft","followers_url":"https://api.github.com/users/fnothaft/followers","following_url":"https://api.github.com/users/fnothaft/following{/other_user}","gists_url":"https://api.github.com/users/fnothaft/gists{/gist_id}","starred_url":"https://api.github.com/users/fnothaft/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/fnothaft/subscriptions","organizations_url":"https://api.github.com/users/fnothaft/orgs","repos_url":"https://api.github.com/users/fnothaft/repos","events_url":"https://api.github.com/users/fnothaft/events{/privacy}","received_events_url":"https://api.github.com/users/fnothaft/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2016-01-24T06:18:56Z","updated_at":"2016-01-24T06:18:58Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/BD2KGenomics/cgl-docker-lib/pulls/76","html_url":"https://github.com/BD2KGenomics/cgl-docker-lib/pull/76","diff_url":"https://github.com/BD2KGenomics/cgl-docker-lib/pull/76.diff","patch_url":"https://github.com/BD2KGenomics/cgl-docker-lib/pull/76.patch"},"body":"Reverts the changes that added the `bwa-postalt` container and modified the `bwa` build. Instead, for alt aware alignment, uses the `bwakit` binary distribution prepared by Heng Li. I've chosen this strategy instead, as the `k8` JavaScript engine used by `bwa-postalt` does not seem to work as compiled –> it fails to allocate memory. I'm not sure why the `bwa-postalt`/`k8` combo in `bwakit` works, but I tried debugging it for several days and assessed that it wasn't worth the time to continue debugging."},"comment":{"url":"https://api.github.com/repos/BD2KGenomics/cgl-docker-lib/issues/comments/174260537","html_url":"https://github.com/BD2KGenomics/cgl-docker-lib/pull/76#issuecomment-174260537","issue_url":"https://api.github.com/repos/BD2KGenomics/cgl-docker-lib/issues/76","id":174260537,"user":{"login":"cgcloud-jenkins","id":12962446,"avatar_url":"https://avatars.githubusercontent.com/u/12962446?v=3","gravatar_id":"","url":"https://api.github.com/users/cgcloud-jenkins","html_url":"https://github.com/cgcloud-jenkins","followers_url":"https://api.github.com/users/cgcloud-jenkins/followers","following_url":"https://api.github.com/users/cgcloud-jenkins/following{/other_user}","gists_url":"https://api.github.com/users/cgcloud-jenkins/gists{/gist_id}","starred_url":"https://api.github.com/users/cgcloud-jenkins/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cgcloud-jenkins/subscriptions","organizations_url":"https://api.github.com/users/cgcloud-jenkins/orgs","repos_url":"https://api.github.com/users/cgcloud-jenkins/repos","events_url":"https://api.github.com/users/cgcloud-jenkins/events{/privacy}","received_events_url":"https://api.github.com/users/cgcloud-jenkins/received_events","type":"User","site_admin":false},"created_at":"2016-01-24T06:18:58Z","updated_at":"2016-01-24T06:18:58Z","body":"Can one of the admins verify this patch?"}}