{"action":"created","issue":{"url":"https://api.github.com/repos/faircloth-lab/phyluce/issues/61","repository_url":"https://api.github.com/repos/faircloth-lab/phyluce","labels_url":"https://api.github.com/repos/faircloth-lab/phyluce/issues/61/labels{/name}","comments_url":"https://api.github.com/repos/faircloth-lab/phyluce/issues/61/comments","events_url":"https://api.github.com/repos/faircloth-lab/phyluce/issues/61/events","html_url":"https://github.com/faircloth-lab/phyluce/issues/61","id":190429000,"number":61,"title":"trimmomatic issue","user":{"login":"confrench33","id":17716287,"avatar_url":"https://avatars.githubusercontent.com/u/17716287?v=3","gravatar_id":"","url":"https://api.github.com/users/confrench33","html_url":"https://github.com/confrench33","followers_url":"https://api.github.com/users/confrench33/followers","following_url":"https://api.github.com/users/confrench33/following{/other_user}","gists_url":"https://api.github.com/users/confrench33/gists{/gist_id}","starred_url":"https://api.github.com/users/confrench33/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/confrench33/subscriptions","organizations_url":"https://api.github.com/users/confrench33/orgs","repos_url":"https://api.github.com/users/confrench33/repos","events_url":"https://api.github.com/users/confrench33/events{/privacy}","received_events_url":"https://api.github.com/users/confrench33/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":2,"created_at":"2016-11-18T21:44:26Z","updated_at":"2016-11-18T22:05:40Z","closed_at":null,"body":"Hello Brian, I'm working through your phyluce tutorial and when I try to run illumiprocessor to clean the reads I get this error:\r\n\r\nTraceback (most recent call last):\r\n  File \"/home/jason/anaconda2/bin/illumiprocessor\", line 17, in <module>\r\n    sys.exit(main())\r\n  File \"/home/jason/anaconda2/lib/python2.7/site-packages/illumiprocessor/cli/main.py\", line 131, in main\r\n    main(args)\r\n  File \"/home/jason/anaconda2/lib/python2.7/site-packages/illumiprocessor/main.py\", line 22, in main\r\n    core.check_dependencies(args)\r\n  File \"/home/jason/anaconda2/lib/python2.7/site-packages/illumiprocessor/core.py\", line 259, in check_dependencies\r\n    java.test_trimmomatic(args.trimmomatic)\r\n  File \"/home/jason/anaconda2/lib/python2.7/site-packages/illumiprocessor/core.py\", line 252, in test_trimmomatic\r\n    \"Trimmomatic does not appear to be installed\"\r\nAssertionError: Trimmomatic does not appear to be installed\r\n\r\n\r\nHowever, \r\n`conda search trimmomatic` returns \r\n\r\n> Fetching package metadata .........\r\ntrimmomatic               *  0.32                          1  http://conda.binstar.org/faircloth-lab \r\n\r\nI know trimmomatic is installed, but for some reason it's not being recognized. I'm running java 1.7 on Ubuntu 16.04, so I don't think java is the problem (I mention this because the core.py program tests for java just before testing for trimmomatic). Do you have any ideas what might be going on? Thanks."},"comment":{"url":"https://api.github.com/repos/faircloth-lab/phyluce/issues/comments/261654385","html_url":"https://github.com/faircloth-lab/phyluce/issues/61#issuecomment-261654385","issue_url":"https://api.github.com/repos/faircloth-lab/phyluce/issues/61","id":261654385,"user":{"login":"brantfaircloth","id":54026,"avatar_url":"https://avatars.githubusercontent.com/u/54026?v=3","gravatar_id":"","url":"https://api.github.com/users/brantfaircloth","html_url":"https://github.com/brantfaircloth","followers_url":"https://api.github.com/users/brantfaircloth/followers","following_url":"https://api.github.com/users/brantfaircloth/following{/other_user}","gists_url":"https://api.github.com/users/brantfaircloth/gists{/gist_id}","starred_url":"https://api.github.com/users/brantfaircloth/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/brantfaircloth/subscriptions","organizations_url":"https://api.github.com/users/brantfaircloth/orgs","repos_url":"https://api.github.com/users/brantfaircloth/repos","events_url":"https://api.github.com/users/brantfaircloth/events{/privacy}","received_events_url":"https://api.github.com/users/brantfaircloth/received_events","type":"User","site_admin":false},"created_at":"2016-11-18T22:05:40Z","updated_at":"2016-11-18T22:05:40Z","body":"also, can you send output of ```java -version```?  thx!"}}
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