{"action":"created","issue":{"url":"https://api.github.com/repos/galaxyproject/galaxy/issues/2344","repository_url":"https://api.github.com/repos/galaxyproject/galaxy","labels_url":"https://api.github.com/repos/galaxyproject/galaxy/issues/2344/labels{/name}","comments_url":"https://api.github.com/repos/galaxyproject/galaxy/issues/2344/comments","events_url":"https://api.github.com/repos/galaxyproject/galaxy/issues/2344/events","html_url":"https://github.com/galaxyproject/galaxy/issues/2344","id":154269632,"number":2344,"title":"Conda resolver issue: _conda/bin/activate: [[: not found","user":{"login":"remimarenco","id":2152858,"avatar_url":"https://avatars.githubusercontent.com/u/2152858?v=3","gravatar_id":"","url":"https://api.github.com/users/remimarenco","html_url":"https://github.com/remimarenco","followers_url":"https://api.github.com/users/remimarenco/followers","following_url":"https://api.github.com/users/remimarenco/following{/other_user}","gists_url":"https://api.github.com/users/remimarenco/gists{/gist_id}","starred_url":"https://api.github.com/users/remimarenco/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/remimarenco/subscriptions","organizations_url":"https://api.github.com/users/remimarenco/orgs","repos_url":"https://api.github.com/users/remimarenco/repos","events_url":"https://api.github.com/users/remimarenco/events{/privacy}","received_events_url":"https://api.github.com/users/remimarenco/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":7,"created_at":"2016-05-11T15:16:31Z","updated_at":"2016-05-19T17:19:36Z","closed_at":null,"body":"Hi,\r\n\r\nI am trying to install locally, on a Galaxy 16.01, a tool ([trfBig on testtoolshed](https://testtoolshed.g2.bx.psu.edu/view/remimarenco/trfbig/3cb9ef4d65d4)) with Conda dependencies. The tool is taking trfBig dependency from [ucsc-trfbig BioConda recipe](https://github.com/bioconda/bioconda-recipes/tree/18694b1f486d64a55587bf71acb0388b635fcb9a/recipes/ucsc-trfbig).\r\n\r\nOnce I installed the tool, successfully if I follow ToolShed output, I have these kinds of errors when I want to start a trfbig job:\r\n\r\n`Tool execution generated the following error message:`\r\n```\r\nFatal error: Exit code 127 ()\r\n/home/remi/Dev/galaxy_remi/database/job_working_directory/000/54/tool_script.sh: 9: /home/remi/Dev/galaxy_remi/database/job_working_directory/000/54/tool_script.sh: trfBig: not found\r\n```\r\n\r\n`The tool produced the following additional output:`\r\n```\r\n/home/remi/Dev/galaxy_remi/database/job_working_directory/000/54/tool_script.sh: 6: /home/remi/Dev/dependency_dir/_conda/bin/activate: [[: not found\r\n/home/remi/Dev/galaxy_remi/database/job_working_directory/000/54/tool_script.sh: 15: /home/remi/Dev/dependency_dir/_conda/bin/activate: [[: not found\r\n/home/remi/Dev/galaxy_remi/database/job_working_directory/000/54/tool_script.sh: 17: /home/remi/Dev/dependency_dir/_conda/bin/activate: [[: not found\r\nOnly bash and zsh are supported\r\n/home/remi/Dev/galaxy_remi/database/job_working_directory/000/54/tool_script.sh: 6: /home/remi/Dev/dependency_dir/_conda/bin/activate: [[: not found\r\n/home/remi/Dev/galaxy_remi/database/job_working_directory/000/54/tool_script.sh: 15: /home/remi/Dev/dependency_dir/_conda/bin/activate: [[: not found\r\n/home/remi/Dev/galaxy_remi/database/job_working_directory/000/54/tool_script.sh: 17: /home/remi/Dev/dependency_dir/_conda/bin/activate: [[: not found\r\nOnly bash and zsh are supported\r\n/home/remi/Dev/galaxy_remi/database/job_working_directory/000/54/galaxy_54.sh: 6: /home/remi/Dev/dependency_dir/_conda/bin/activate: [[: not found\r\n/home/remi/Dev/galaxy_remi/database/job_working_directory/000/54/galaxy_54.sh: 15: /home/remi/Dev/dependency_dir/_conda/bin/activate: [[: not found\r\n/home/remi/Dev/galaxy_remi/database/job_working_directory/000/54/galaxy_54.sh: 17: /home/remi/Dev/dependency_dir/_conda/bin/activate: [[: not found\r\n```\r\n\r\nDo you know why the tool is not working and why I have these outputs about conda virtualenv?"},"comment":{"url":"https://api.github.com/repos/galaxyproject/galaxy/issues/comments/220392763","html_url":"https://github.com/galaxyproject/galaxy/issues/2344#issuecomment-220392763","issue_url":"https://api.github.com/repos/galaxyproject/galaxy/issues/2344","id":220392763,"user":{"login":"remimarenco","id":2152858,"avatar_url":"https://avatars.githubusercontent.com/u/2152858?v=3","gravatar_id":"","url":"https://api.github.com/users/remimarenco","html_url":"https://github.com/remimarenco","followers_url":"https://api.github.com/users/remimarenco/followers","following_url":"https://api.github.com/users/remimarenco/following{/other_user}","gists_url":"https://api.github.com/users/remimarenco/gists{/gist_id}","starred_url":"https://api.github.com/users/remimarenco/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/remimarenco/subscriptions","organizations_url":"https://api.github.com/users/remimarenco/orgs","repos_url":"https://api.github.com/users/remimarenco/repos","events_url":"https://api.github.com/users/remimarenco/events{/privacy}","received_events_url":"https://api.github.com/users/remimarenco/received_events","type":"User","site_admin":false},"created_at":"2016-05-19T17:19:36Z","updated_at":"2016-05-19T17:19:36Z","body":"Ok reinstalled everything on my Virtual Machine and seems fine. Closing as I can't reproduce."}}