{"action":"created","issue":{"url":"https://api.github.com/repos/galaxyproject/tools-devteam/issues/65","labels_url":"https://api.github.com/repos/galaxyproject/tools-devteam/issues/65/labels{/name}","comments_url":"https://api.github.com/repos/galaxyproject/tools-devteam/issues/65/comments","events_url":"https://api.github.com/repos/galaxyproject/tools-devteam/issues/65/events","html_url":"https://github.com/galaxyproject/tools-devteam/issues/65","id":58832062,"number":65,"title":"weblogo3 tool missing dependency on numpy","user":{"login":"bcclaywell","id":1108400,"avatar_url":"https://avatars.githubusercontent.com/u/1108400?v=3","gravatar_id":"","url":"https://api.github.com/users/bcclaywell","html_url":"https://github.com/bcclaywell","followers_url":"https://api.github.com/users/bcclaywell/followers","following_url":"https://api.github.com/users/bcclaywell/following{/other_user}","gists_url":"https://api.github.com/users/bcclaywell/gists{/gist_id}","starred_url":"https://api.github.com/users/bcclaywell/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bcclaywell/subscriptions","organizations_url":"https://api.github.com/users/bcclaywell/orgs","repos_url":"https://api.github.com/users/bcclaywell/repos","events_url":"https://api.github.com/users/bcclaywell/events{/privacy}","received_events_url":"https://api.github.com/users/bcclaywell/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2015-02-25T00:43:58Z","updated_at":"2015-02-25T07:22:20Z","closed_at":null,"body":"The weblogo3 tool was failing for us, with the `rgWebLogo.py` wrapper reporting that weblogo was returning exit code 1. At the command line I duplicated the job environment and dependency shell commands and was able to reproduce the error:\r\n\r\n```\r\n## rgWebLogo3.py error - executing weblogo -F jpeg -c auto -o /home/galaxy/tmp/logo.jpg -U bits -t \"test\" -f /home/galaxy/tmp/test.fasta -s medium returned error code 1\r\n## This may be a data problem or a tool dependency (weblogo) installation problem\r\n## Please ensure weblogo is correctly installed and working on the command line -see http://code.google.com/p/weblogo\r\n```\r\n\r\nI then tried running the above weblogo command directly:\r\n\r\n```\r\nTraceback (most recent call last):\r\n  File \"/mnt/scdata/scdata_03/galaxy/containers/galaxy-qa/tool_deps/weblogo/3.3/devteam/package_weblogo_3_3/648e4b32f15c/weblogo\", line 56, in <module>\r\n    import weblogolib._cli\r\n  File \"/mnt/scdata/scdata_03/galaxy/containers/galaxy-qa/export/tool_deps/weblogo/3.3/devteam/package_weblogo_3_3/648e4b32f15c/weblogolib/__init__.py\", line 108, in <module>\r\n    from numpy import array, asarray, float64, ones, zeros, int32,all,any, shape\r\nImportError: No module named numpy\r\n```\r\n\r\nAs a quick fix, I added a package dependency requirement for numpy to `rgWebLogo3.xml` and reloaded the tool in Galaxy, after which the tool worked properly."},"comment":{"url":"https://api.github.com/repos/galaxyproject/tools-devteam/issues/comments/75916678","html_url":"https://github.com/galaxyproject/tools-devteam/issues/65#issuecomment-75916678","issue_url":"https://api.github.com/repos/galaxyproject/tools-devteam/issues/65","id":75916678,"user":{"login":"bgruening","id":469983,"avatar_url":"https://avatars.githubusercontent.com/u/469983?v=3","gravatar_id":"","url":"https://api.github.com/users/bgruening","html_url":"https://github.com/bgruening","followers_url":"https://api.github.com/users/bgruening/followers","following_url":"https://api.github.com/users/bgruening/following{/other_user}","gists_url":"https://api.github.com/users/bgruening/gists{/gist_id}","starred_url":"https://api.github.com/users/bgruening/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bgruening/subscriptions","organizations_url":"https://api.github.com/users/bgruening/orgs","repos_url":"https://api.github.com/users/bgruening/repos","events_url":"https://api.github.com/users/bgruening/events{/privacy}","received_events_url":"https://api.github.com/users/bgruening/received_events","type":"User","site_admin":false},"created_at":"2015-02-25T07:22:20Z","updated_at":"2015-02-25T07:22:20Z","body":"Brian; thanks for reporting. I pushed a fix, this will be included in the ToolShed as soon as possible."}}