{"action":"created","issue":{"url":"https://api.github.com/repos/gkno/gkno_launcher/issues/68","repository_url":"https://api.github.com/repos/gkno/gkno_launcher","labels_url":"https://api.github.com/repos/gkno/gkno_launcher/issues/68/labels{/name}","comments_url":"https://api.github.com/repos/gkno/gkno_launcher/issues/68/comments","events_url":"https://api.github.com/repos/gkno/gkno_launcher/issues/68/events","html_url":"https://github.com/gkno/gkno_launcher/issues/68","id":161256351,"number":68,"title":"Error Building GKNO due to tutorial retrieval failure","user":{"login":"mcnaircm","id":20050450,"avatar_url":"https://avatars.githubusercontent.com/u/20050450?v=3","gravatar_id":"","url":"https://api.github.com/users/mcnaircm","html_url":"https://github.com/mcnaircm","followers_url":"https://api.github.com/users/mcnaircm/followers","following_url":"https://api.github.com/users/mcnaircm/following{/other_user}","gists_url":"https://api.github.com/users/mcnaircm/gists{/gist_id}","starred_url":"https://api.github.com/users/mcnaircm/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mcnaircm/subscriptions","organizations_url":"https://api.github.com/users/mcnaircm/orgs","repos_url":"https://api.github.com/users/mcnaircm/repos","events_url":"https://api.github.com/users/mcnaircm/events{/privacy}","received_events_url":"https://api.github.com/users/mcnaircm/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":5,"created_at":"2016-06-20T18:00:56Z","updated_at":"2016-11-25T17:47:32Z","closed_at":null,"body":"I am currently having an issue in building gkno, and weirdly enough it seems to be with the retrieval of the tutorial after everything esle is done which terminates the process.  The following is what I see when I try to run the build:\n./gkno build                                                                                                                                                                                                 [ 1:35PM]\n# \n\n  University of Utah gkno package\n\n  version:    2.57.0\n  date:       June 2016\n#   git commit: de31cc53dad6c57e73a2d7e8110487f10339abdb\n\nChecking dependencies...done.\nInitializing component data...done.\nBuilding tools: \n  bamaddrg...done.\n  bamtools...done.\n  bedtools...done.\n  blast...done.\n  bwa...done.\n  freebayes...done.\n  htslib...done.\n  samtools...done.\n  pindel...done.\n  libStatGen...done.\n  bamUtil...done.\n  fastQValidator...done.\n  qplot...done.\n  verifyBamID...done.\n  mosaik...done.\n  mutatrix...done.\n  picard...done.\n  samblaster...done.\n  seqan...done.\n  snpEff...done.\n  tabix...done.\n  tangram...done.\n  vcflib...done.\n  vt...done.\n  wham...done.\nFetching default resources:\n  tutorial:\n    Downloading files...  0%ERROR: Could not retrieve file at http://marth-award.genetics.utah.edu:8089/version_10.tar.gz\nERROR:  See logs/build_tutorial.\\* files for more details.\n# \n#   TERMINATED: Errors found in running gkno.  See specific error messages above for resolution.\n\nI'm not really sure why not having the tutorial file would terminate the whole process, but there you have it.  Any help in figuring out how to get around this issue would be much appreciated!\n\nCheers,\nChris\n"},"comment":{"url":"https://api.github.com/repos/gkno/gkno_launcher/issues/comments/263004139","html_url":"https://github.com/gkno/gkno_launcher/issues/68#issuecomment-263004139","issue_url":"https://api.github.com/repos/gkno/gkno_launcher/issues/68","id":263004139,"user":{"login":"AlistairNWard","id":523111,"avatar_url":"https://avatars.githubusercontent.com/u/523111?v=3","gravatar_id":"","url":"https://api.github.com/users/AlistairNWard","html_url":"https://github.com/AlistairNWard","followers_url":"https://api.github.com/users/AlistairNWard/followers","following_url":"https://api.github.com/users/AlistairNWard/following{/other_user}","gists_url":"https://api.github.com/users/AlistairNWard/gists{/gist_id}","starred_url":"https://api.github.com/users/AlistairNWard/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/AlistairNWard/subscriptions","organizations_url":"https://api.github.com/users/AlistairNWard/orgs","repos_url":"https://api.github.com/users/AlistairNWard/repos","events_url":"https://api.github.com/users/AlistairNWard/events{/privacy}","received_events_url":"https://api.github.com/users/AlistairNWard/received_events","type":"User","site_admin":false},"created_at":"2016-11-25T17:47:32Z","updated_at":"2016-11-25T17:47:32Z","body":"gkno has installed successfully. Only those tools marked as failed will not\nbe executable (i.e. pindel, mosaik, mutatrix and wham). These are not\ncommon tools to use, so this should not present a problem to using the\nmajority of the gkno pipelines. If you type run the gkno executable file,\nyou should see that gkno runs and you can choose different pipelines to\nrun. Some help is provided at gkno.me, or you can contact me for specific\nhelp and guidance.\n\n\nAlistair Ward, PhD\nDirector, Research and Science\nDepartment of Human Genetics\nUSTAR Center for Genetic Discovery\nEccles Institute of Human Genetics\nUniversity of Utah School of Medicine​\n15 North 2030 East, Room 7140\nSalt Lake City, UT 84112-5330\n\nCo-founder, Frameshift labs, LLC\n\nOn Fri, Nov 25, 2016 at 3:42 AM, hideoimamura <notifications@github.com>\nwrote:\n\n> Hi Alistair,\n> I have the same problem. I am repeated this installation a few times but I\n> got to the same point.\n> thank you,\n> Hideo\n>\n> mac-C02N1289FH05:gkno_launcher himamura$ ./gkno build\n>\n> ========================================================\n> University of Utah gkno package\n> version: 2.63.7\n> date: November 2016\n> git commit: 0274e25\n> <https://github.com/gkno/gkno_launcher/commit/0274e25cdbfe8e892a1db1f29b31d4f99d451758>\n>\n> Checking dependencies...done.\n> Initializing component data...\n> done.\n> Building tools:\n> bamaddrg...done.\n> bamtools...done.\n> bedtools...done.\n> blast...done.\n> bwa...done.\n> freebayes...done.\n> htslib...done.\n> samtools...done.\n> pindel...ERROR: See logs/build_pindel.* files for more details.\n> libStatGen...done.\n> bamUtil...done.\n> fastQValidator...done.\n> qplot...done.\n> verifyBamID...done.\n> mosaik...ERROR: See logs/build_mosaik.* files for more details.\n> mutatrix...ERROR: See logs/build_mutatrix.* files for more details.\n> picard...done.\n> samblaster...done.\n> seqan...done.\n> snpEff...done.\n> tabix...done.\n> tangram...done.\n> vcflib...done.\n> vt...done.\n> wham...ERROR: See logs/build_wham.* files for more details.\n> Fetching default resources:\n> tutorial:\n> Downloading files... 0%\n>\n> —\n> You are receiving this because you commented.\n> Reply to this email directly, view it on GitHub\n> <https://github.com/gkno/gkno_launcher/issues/68#issuecomment-262906700>,\n> or mute the thread\n> <https://github.com/notifications/unsubscribe-auth/AAf7Z3Wau1hIKoZ0ZfmlMU5a9BxW4_S7ks5rBp-IgaJpZM4I59g1>\n> .\n>\n"}}
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