{"action":"created","issue":{"url":"https://api.github.com/repos/genome/gms/issues/47","labels_url":"https://api.github.com/repos/genome/gms/issues/47/labels{/name}","comments_url":"https://api.github.com/repos/genome/gms/issues/47/comments","events_url":"https://api.github.com/repos/genome/gms/issues/47/events","html_url":"https://github.com/genome/gms/issues/47","id":23421145,"number":47,"title":"Somatic variation fails because of inability to find GATK","user":{"login":"malachig","id":856728,"avatar_url":"https://avatars.githubusercontent.com/u/856728?v=3","gravatar_id":"","url":"https://api.github.com/users/malachig","html_url":"https://github.com/malachig","followers_url":"https://api.github.com/users/malachig/followers","following_url":"https://api.github.com/users/malachig/following{/other_user}","gists_url":"https://api.github.com/users/malachig/gists{/gist_id}","starred_url":"https://api.github.com/users/malachig/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/malachig/subscriptions","organizations_url":"https://api.github.com/users/malachig/orgs","repos_url":"https://api.github.com/users/malachig/repos","events_url":"https://api.github.com/users/malachig/events{/privacy}","received_events_url":"https://api.github.com/users/malachig/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/genome/gms/labels/bug","name":"bug","color":"fc2929"},{"url":"https://api.github.com/repos/genome/gms/labels/license%20issue","name":"license issue","color":"eb6420"}],"state":"open","locked":false,"assignee":{"login":"gatoravi","id":764948,"avatar_url":"https://avatars.githubusercontent.com/u/764948?v=3","gravatar_id":"","url":"https://api.github.com/users/gatoravi","html_url":"https://github.com/gatoravi","followers_url":"https://api.github.com/users/gatoravi/followers","following_url":"https://api.github.com/users/gatoravi/following{/other_user}","gists_url":"https://api.github.com/users/gatoravi/gists{/gist_id}","starred_url":"https://api.github.com/users/gatoravi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/gatoravi/subscriptions","organizations_url":"https://api.github.com/users/gatoravi/orgs","repos_url":"https://api.github.com/users/gatoravi/repos","events_url":"https://api.github.com/users/gatoravi/events{/privacy}","received_events_url":"https://api.github.com/users/gatoravi/received_events","type":"User","site_admin":false},"milestone":null,"comments":10,"created_at":"2013-11-27T23:09:05Z","updated_at":"2015-03-18T15:05:25Z","closed_at":null,"body":"The first test of somatic-variation hit an error after about 1 min.  The top of the error log looks like this:\r\n\r\n```\r\n2013-11-27 16:41:10-0600 clia1: Executing detect variants step\r\n2013-11-27 16:41:14-0600 clia1: 2013/11/27 16:41:14 Genome::Sys: Failed to find jar GenomeAnalysisTK at version 2.4\r\n2013-11-27 16:41:14-0600 clia1: ERROR: Failed to find jar GenomeAnalysisTK at version 2.4\r\n2013-11-27 16:41:14-0600 clia1: 2013/11/27 16:41:14 Genome::Model::Tools::DetectVariants2::Strategy id((gatk-somatic-indel 5336 filtered by false-indel v1 [--bam-readcount-version 0.4 --bam-readcount-min-base-quality 15]) unique union (pindel 0.5 filtered by pindel-somatic-calls v1 then pindel-vaf-filter v1 [--variant-freq-cutoff=0.08] then pindel-read-support v1) unique union (varscan-somatic 2.2.6 filtered by varscan-high-confidence-indel v1 then false-indel v1 [--bam-readcount-version 0.4 --bam-readcount-min-base-quality 15]) unique union (strelka 0.4.6.2 [isSkipDepthFilters = 1])): Could not call has_version on the class Genome::Model::Tools::DetectVariants2::GatkSomaticIndel\r\n2013-11-27 16:41:14-0600 clia1: ERROR: Could not call has_version on the class Genome::Model::Tools::DetectVariants2::GatkSomaticIndel\r\n2013-11-27 16:41:14-0600 clia1: Command module died or returned undef.\r\n```\r\n\r\nWe need to determine how software versions are found in the part of DV2...\r\n"},"comment":{"url":"https://api.github.com/repos/genome/gms/issues/comments/83013940","html_url":"https://github.com/genome/gms/issues/47#issuecomment-83013940","issue_url":"https://api.github.com/repos/genome/gms/issues/47","id":83013940,"user":{"login":"gatoravi","id":764948,"avatar_url":"https://avatars.githubusercontent.com/u/764948?v=3","gravatar_id":"","url":"https://api.github.com/users/gatoravi","html_url":"https://github.com/gatoravi","followers_url":"https://api.github.com/users/gatoravi/followers","following_url":"https://api.github.com/users/gatoravi/following{/other_user}","gists_url":"https://api.github.com/users/gatoravi/gists{/gist_id}","starred_url":"https://api.github.com/users/gatoravi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/gatoravi/subscriptions","organizations_url":"https://api.github.com/users/gatoravi/orgs","repos_url":"https://api.github.com/users/gatoravi/repos","events_url":"https://api.github.com/users/gatoravi/events{/privacy}","received_events_url":"https://api.github.com/users/gatoravi/received_events","type":"User","site_admin":false},"created_at":"2015-03-18T15:05:25Z","updated_at":"2015-03-18T15:05:25Z","body":"not sure where to bring this up on master, Issues seem to be disabled for that repo. cc'ing @nnutter for ideas."}}