{"action":"created","issue":{"url":"https://api.github.com/repos/galaxyproject/tools-iuc/issues/967","repository_url":"https://api.github.com/repos/galaxyproject/tools-iuc","labels_url":"https://api.github.com/repos/galaxyproject/tools-iuc/issues/967/labels{/name}","comments_url":"https://api.github.com/repos/galaxyproject/tools-iuc/issues/967/comments","events_url":"https://api.github.com/repos/galaxyproject/tools-iuc/issues/967/events","html_url":"https://github.com/galaxyproject/tools-iuc/pull/967","id":179419553,"number":967,"title":"Mothur fixes (WIPish)","user":{"login":"shiltemann","id":2563865,"avatar_url":"https://avatars.githubusercontent.com/u/2563865?v=3","gravatar_id":"","url":"https://api.github.com/users/shiltemann","html_url":"https://github.com/shiltemann","followers_url":"https://api.github.com/users/shiltemann/followers","following_url":"https://api.github.com/users/shiltemann/following{/other_user}","gists_url":"https://api.github.com/users/shiltemann/gists{/gist_id}","starred_url":"https://api.github.com/users/shiltemann/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/shiltemann/subscriptions","organizations_url":"https://api.github.com/users/shiltemann/orgs","repos_url":"https://api.github.com/users/shiltemann/repos","events_url":"https://api.github.com/users/shiltemann/events{/privacy}","received_events_url":"https://api.github.com/users/shiltemann/received_events","type":"User","site_admin":false},"labels":[{"id":176088515,"url":"https://api.github.com/repos/galaxyproject/tools-iuc/labels/reviewer%20needed","name":"reviewer needed","color":"eb6420","default":false}],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":2,"created_at":"2016-09-27T07:45:07Z","updated_at":"2016-12-14T17:18:56Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/galaxyproject/tools-iuc/pulls/967","html_url":"https://github.com/galaxyproject/tools-iuc/pull/967","diff_url":"https://github.com/galaxyproject/tools-iuc/pull/967.diff","patch_url":"https://github.com/galaxyproject/tools-iuc/pull/967.patch"},"body":"adding fixes here as I/others encounter them, more will undoubtedly be added, we can leave this open until an update in (test)toolshed is desired\r\n\r\nTODO:\r\n- [x] fix broken links\r\n- [x] add tool for get.communitytype command\r\n- [x] add tool for lefse command\r\n- [x] add tool for classify.rf command\r\n\r\nP.S. this won't pass travis testing as the linting is triggered 125 x 125 times and it times out before it even gets to planemo test command (galaxyproject/planemo/issues/564) (and right now mothur site is down so URLs wont validate either)"},"comment":{"url":"https://api.github.com/repos/galaxyproject/tools-iuc/issues/comments/267095724","html_url":"https://github.com/galaxyproject/tools-iuc/pull/967#issuecomment-267095724","issue_url":"https://api.github.com/repos/galaxyproject/tools-iuc/issues/967","id":267095724,"user":{"login":"blankenberg","id":1231190,"avatar_url":"https://avatars.githubusercontent.com/u/1231190?v=3","gravatar_id":"","url":"https://api.github.com/users/blankenberg","html_url":"https://github.com/blankenberg","followers_url":"https://api.github.com/users/blankenberg/followers","following_url":"https://api.github.com/users/blankenberg/following{/other_user}","gists_url":"https://api.github.com/users/blankenberg/gists{/gist_id}","starred_url":"https://api.github.com/users/blankenberg/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/blankenberg/subscriptions","organizations_url":"https://api.github.com/users/blankenberg/orgs","repos_url":"https://api.github.com/users/blankenberg/repos","events_url":"https://api.github.com/users/blankenberg/events{/privacy}","received_events_url":"https://api.github.com/users/blankenberg/received_events","type":"User","site_admin":false},"created_at":"2016-12-14T17:18:56Z","updated_at":"2016-12-14T17:18:56Z","body":"Was trying this locally using conda, but looks like the dependencies might be broken due to lib boost version mismatch (using `make.group`):\r\n```\r\nmothur: error while loading shared libraries: libboost_iostreams.so.1.57.0: cannot open shared object file: No such file or directory\r\nmothur: error while loading shared libraries: libboost_iostreams.so.1.57.0: cannot open shared object file: No such file or directory\r\nsed: couldn't flush stdout: Broken pipe\r\n```\r\n\r\n```\r\nThe following NEW packages will be INSTALLED:\r\n\r\n    boost:      1.62.0-py35_0   \r\n    certifi:    2016.9.26-py35_0\r\n    icu:        56.1-4          \r\n    mothur:     1.36.1-0        \r\n    ncurses:    5.9-10          \r\n    openssl:    1.0.2j-0        \r\n    pip:        9.0.1-py35_1    \r\n    python:     3.5.2-2         \r\n    readline:   6.2-2           \r\n    setuptools: 29.0.1-py35_1   \r\n    sqlite:     3.13.0-1        \r\n    tk:         8.5.19-1        \r\n    wheel:      0.29.0-py35_0   \r\n    xz:         5.2.2-0         \r\n    zlib:       1.2.8-3     \r\n```\r\n\r\nWill see if I can find some time to dig further.\r\n\r\n(Also ended up with Green Dataset, instead of error, will take a look at that as well.)"}}
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