{"action":"created","issue":{"url":"https://api.github.com/repos/ioquatix/script-runner/issues/39","labels_url":"https://api.github.com/repos/ioquatix/script-runner/issues/39/labels{/name}","comments_url":"https://api.github.com/repos/ioquatix/script-runner/issues/39/comments","events_url":"https://api.github.com/repos/ioquatix/script-runner/issues/39/events","html_url":"https://github.com/ioquatix/script-runner/issues/39","id":100282599,"number":39,"title":"Using bad interpreter","user":{"login":"maasha","id":1158057,"avatar_url":"https://avatars.githubusercontent.com/u/1158057?v=3","gravatar_id":"","url":"https://api.github.com/users/maasha","html_url":"https://github.com/maasha","followers_url":"https://api.github.com/users/maasha/followers","following_url":"https://api.github.com/users/maasha/following{/other_user}","gists_url":"https://api.github.com/users/maasha/gists{/gist_id}","starred_url":"https://api.github.com/users/maasha/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/maasha/subscriptions","organizations_url":"https://api.github.com/users/maasha/orgs","repos_url":"https://api.github.com/users/maasha/repos","events_url":"https://api.github.com/users/maasha/events{/privacy}","received_events_url":"https://api.github.com/users/maasha/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":7,"created_at":"2015-08-11T10:29:37Z","updated_at":"2015-08-20T07:46:44Z","closed_at":null,"body":"I would like to run a particular Ruby script using script-runner:\r\n\r\n```\r\n#!/usr/bin/env ruby\r\n\r\nrequire 'biopieces'\r\n\r\np = BP.new.\r\n    read_fastq(first: 100_000, input: 'test_R1.fq.gz', encoding: :base_33).\r\n    run(progress: true)\r\n\r\npp p.status\r\n```\r\n\r\nIt works fine from the command line:\r\n\r\n```\r\n/usr/bin/env ruby /Users/maasha/scratch/test.bp\r\n```\r\n\r\nHowever script-running in atom says:\r\n\r\n```\r\nScript Runner: test.bp\r\n\r\nRunning: /usr/bin/env ruby /Users/maasha/scratch/test.bp (pgid 2279)\r\n/System/Library/Frameworks/Ruby.framework/Versions/2.0/usr/lib/ruby/2.0.0/rubygems/core_ext/kernel_require.rb:55:in `require': cannot load such file -- biopieces (LoadError)\r\n\tfrom /System/Library/Frameworks/Ruby.framework/Versions/2.0/usr/lib/ruby/2.0.0/rubygems/core_ext/kernel_require.rb:55:in `require'\r\n\tfrom /Users/maasha/scratch/test.bp:3:in `<main>'\r\nExited with status 1 after 0.065 seconds\r\n```\r\n\r\nIt is evidently using the systems Ruby and not the one in the environment as specified by the hash-bang line:\r\n\r\n```\r\n$ env ruby --version\r\nruby 2.2.0p0 (2014-12-25 revision 49005) [x86_64-darwin14]\r\n```"},"comment":{"url":"https://api.github.com/repos/ioquatix/script-runner/issues/comments/132922024","html_url":"https://github.com/ioquatix/script-runner/issues/39#issuecomment-132922024","issue_url":"https://api.github.com/repos/ioquatix/script-runner/issues/39","id":132922024,"user":{"login":"ioquatix","id":30030,"avatar_url":"https://avatars.githubusercontent.com/u/30030?v=3","gravatar_id":"","url":"https://api.github.com/users/ioquatix","html_url":"https://github.com/ioquatix","followers_url":"https://api.github.com/users/ioquatix/followers","following_url":"https://api.github.com/users/ioquatix/following{/other_user}","gists_url":"https://api.github.com/users/ioquatix/gists{/gist_id}","starred_url":"https://api.github.com/users/ioquatix/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ioquatix/subscriptions","organizations_url":"https://api.github.com/users/ioquatix/orgs","repos_url":"https://api.github.com/users/ioquatix/repos","events_url":"https://api.github.com/users/ioquatix/events{/privacy}","received_events_url":"https://api.github.com/users/ioquatix/received_events","type":"User","site_admin":false},"created_at":"2015-08-20T07:46:44Z","updated_at":"2015-08-20T07:46:44Z","body":"I don't see anything in there relating to homebrew.. what is the normal output of `env`?"}}