{"action":"created","issue":{"url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/796","labels_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/796/labels{/name}","comments_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/796/comments","events_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/796/events","html_url":"https://github.com/chapmanb/bcbio-nextgen/issues/796","id":63234666,"number":796,"title":"Kraken installation fails due to hardcoded version path","user":{"login":"schelhorn","id":5024959,"avatar_url":"https://avatars.githubusercontent.com/u/5024959?v=3","gravatar_id":"","url":"https://api.github.com/users/schelhorn","html_url":"https://github.com/schelhorn","followers_url":"https://api.github.com/users/schelhorn/followers","following_url":"https://api.github.com/users/schelhorn/following{/other_user}","gists_url":"https://api.github.com/users/schelhorn/gists{/gist_id}","starred_url":"https://api.github.com/users/schelhorn/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/schelhorn/subscriptions","organizations_url":"https://api.github.com/users/schelhorn/orgs","repos_url":"https://api.github.com/users/schelhorn/repos","events_url":"https://api.github.com/users/schelhorn/events{/privacy}","received_events_url":"https://api.github.com/users/schelhorn/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2015-03-20T14:11:50Z","updated_at":"2015-03-20T19:09:18Z","closed_at":null,"body":"After upgrading bcbio to install kraken with `bcbio_nextgen.py upgrade -u development --tools --data --toolplus kraken` the installation of kraken fails due to a hardcoded version path in in `bcbio/install.py`. In line `474` it says `shutil.move(os.path.join(kraken, \"minikraken_20140330\"), os.path.join(kraken, \"minikraken\"))`; however, the kraken archive seems to contain a newer `minikraken_20141208` instead, resulting in an `IOError: [Errno 2] No such file or directory: 'PATH_TOBCBIO_LIB/genomes/kraken/minikraken_20140330'`. Perhaps one could do the directory move on a wildcard basis instead?"},"comment":{"url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/comments/84102654","html_url":"https://github.com/chapmanb/bcbio-nextgen/issues/796#issuecomment-84102654","issue_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/796","id":84102654,"user":{"login":"lpantano","id":1621788,"avatar_url":"https://avatars.githubusercontent.com/u/1621788?v=3","gravatar_id":"","url":"https://api.github.com/users/lpantano","html_url":"https://github.com/lpantano","followers_url":"https://api.github.com/users/lpantano/followers","following_url":"https://api.github.com/users/lpantano/following{/other_user}","gists_url":"https://api.github.com/users/lpantano/gists{/gist_id}","starred_url":"https://api.github.com/users/lpantano/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lpantano/subscriptions","organizations_url":"https://api.github.com/users/lpantano/orgs","repos_url":"https://api.github.com/users/lpantano/repos","events_url":"https://api.github.com/users/lpantano/events{/privacy}","received_events_url":"https://api.github.com/users/lpantano/received_events","type":"User","site_admin":false},"created_at":"2015-03-20T19:09:18Z","updated_at":"2015-03-20T19:09:18Z","body":"I update with a new function that will check the date of the tar file and the current kraken folder and will update if it is older. d59e2b1\r\nIf there is any problem, let me know. thanks! "}}