{"action":"created","comment":{"url":"https://api.github.com/repos/broadinstitute/cromwell/pulls/comments/32444984","id":32444984,"diff_hunk":"@@ -75,4 +97,71 @@ class LocalBackend extends Backend {\n       taskOutput.name -> rawValue.map { possiblyAutoConvertedValue(taskOutput, _) }\n     }.toMap\n   }\n+\n+  /**\n+   * Creates host execution directory, inputs path, and outputs path.  Stages any input files into the workflow-inputs\n+   * directory and localizes their paths relative to the container.\n+   */\n+  override def initializeWorkflow(workflow: WorkflowDescriptor, actualInputs: Map[FullyQualifiedName, WdlValue]): Map[FullyQualifiedName, WdlValue] = {\n+    val hostExecutionDirectory = hostExecutionPath(workflow).toFile\n+    hostExecutionDirectory.mkdirs()\n+\n+    val hostExecutionAbsolutePath = hostExecutionDirectory.getAbsolutePath\n+    val hostInputsPath = Paths.get(hostExecutionAbsolutePath, \"workflow-inputs\")","path":"src/main/scala/cromwell/engine/backend/local/LocalBackend.scala","position":104,"original_position":104,"commit_id":"b0848f1b61e51e24bdd837f24c27b0abfae39dad","original_commit_id":"b0848f1b61e51e24bdd837f24c27b0abfae39dad","user":{"login":"geoffjentry","id":961771,"avatar_url":"https://avatars.githubusercontent.com/u/961771?v=3","gravatar_id":"","url":"https://api.github.com/users/geoffjentry","html_url":"https://github.com/geoffjentry","followers_url":"https://api.github.com/users/geoffjentry/followers","following_url":"https://api.github.com/users/geoffjentry/following{/other_user}","gists_url":"https://api.github.com/users/geoffjentry/gists{/gist_id}","starred_url":"https://api.github.com/users/geoffjentry/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/geoffjentry/subscriptions","organizations_url":"https://api.github.com/users/geoffjentry/orgs","repos_url":"https://api.github.com/users/geoffjentry/repos","events_url":"https://api.github.com/users/geoffjentry/events{/privacy}","received_events_url":"https://api.github.com/users/geoffjentry/received_events","type":"User","site_admin":false},"body":"I have the slightest of preferences for the `workflow-` variant","created_at":"2015-06-15T17:30:12Z","updated_at":"2015-06-15T17:30:12Z","html_url":"https://github.com/broadinstitute/cromwell/pull/43#discussion_r32444984","pull_request_url":"https://api.github.com/repos/broadinstitute/cromwell/pulls/43","_links":{"self":{"href":"https://api.github.com/repos/broadinstitute/cromwell/pulls/comments/32444984"},"html":{"href":"https://github.com/broadinstitute/cromwell/pull/43#discussion_r32444984"},"pull_request":{"href":"https://api.github.com/repos/broadinstitute/cromwell/pulls/43"}}},"pull_request":{"url":"https://api.github.com/repos/broadinstitute/cromwell/pulls/43","id":37618069,"html_url":"https://github.com/broadinstitute/cromwell/pull/43","diff_url":"https://github.com/broadinstitute/cromwell/pull/43.diff","patch_url":"https://github.com/broadinstitute/cromwell/pull/43.patch","issue_url":"https://api.github.com/repos/broadinstitute/cromwell/issues/43","number":43,"state":"open","locked":false,"title":"DO NOT MERGE - EPIC CI FAIL First cut of Dockerization, currently always tries to run with a Docker backend.","user":{"login":"mcovarr","id":10790523,"avatar_url":"https://avatars.githubusercontent.com/u/10790523?v=3","gravatar_id":"","url":"https://api.github.com/users/mcovarr","html_url":"https://github.com/mcovarr","followers_url":"https://api.github.com/users/mcovarr/followers","following_url":"https://api.github.com/users/mcovarr/following{/other_user}","gists_url":"https://api.github.com/users/mcovarr/gists{/gist_id}","starred_url":"https://api.github.com/users/mcovarr/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mcovarr/subscriptions","organizations_url":"https://api.github.com/users/mcovarr/orgs","repos_url":"https://api.github.com/users/mcovarr/repos","events_url":"https://api.github.com/users/mcovarr/events{/privacy}","received_events_url":"https://api.github.com/users/mcovarr/received_events","type":"User","site_admin":false},"body":"Bombs out in Travis due to lack of Docker.  Maybe Jenkins or CircleCI can handle this?  Also missing parsing of runtime sections of tasks, so this is currently hardcoded to always try to use Docker.\r\n","created_at":"2015-06-13T02:58:57Z","updated_at":"2015-06-15T17:30:12Z","closed_at":null,"merged_at":null,"merge_commit_sha":"2956fdd09a1b8c848f870cda544275c6a9703bb2","assignee":null,"milestone":null,"commits_url":"https://api.github.com/repos/broadinstitute/cromwell/pulls/43/commits","review_comments_url":"https://api.github.com/repos/broadinstitute/cromwell/pulls/43/comments","review_comment_url":"https://api.github.com/repos/broadinstitute/cromwell/pulls/comments{/number}","comments_url":"https://api.github.com/repos/broadinstitute/cromwell/issues/43/comments","statuses_url":"https://api.github.com/repos/broadinstitute/cromwell/statuses/b0848f1b61e51e24bdd837f24c27b0abfae39dad","head":{"label":"broadinstitute:mlc_docker_backend","ref":"mlc_docker_backend","sha":"b0848f1b61e51e24bdd837f24c27b0abfae39dad","user":{"login":"broadinstitute","id":393552,"avatar_url":"https://avatars.githubusercontent.com/u/393552?v=3","gravatar_id":"","url":"https://api.github.com/users/broadinstitute","html_url":"https://github.com/broadinstitute","followers_url":"https://api.github.com/users/broadinstitute/followers","following_url":"https://api.github.com/users/broadinstitute/following{/other_user}","gists_url":"https://api.github.com/users/broadinstitute/gists{/gist_id}","starred_url":"https://api.github.com/users/broadinstitute/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/broadinstitute/subscriptions","organizations_url":"https://api.github.com/users/broadinstitute/orgs","repos_url":"https://api.github.com/users/broadinstitute/repos","events_url":"https://api.github.com/users/broadinstitute/events{/privacy}","received_events_url":"https://api.github.com/users/broadinstitute/received_events","type":"Organization","site_admin":false},"repo":{"id":34136406,"name":"cromwell","full_name":"broadinstitute/cromwell","owner":{"login":"broadinstitute","id":393552,"avatar_url":"https://avatars.githubusercontent.com/u/393552?v=3","gravatar_id":"","url":"https://api.github.com/users/broadinstitute","html_url":"https://github.com/broadinstitute","followers_url":"https://api.github.com/users/broadinstitute/followers","following_url":"https://api.github.com/users/broadinstitute/following{/other_user}","gists_url":"https://api.github.com/users/broadinstitute/gists{/gist_id}","starred_url":"https://api.github.com/users/broadinstitute/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/broadinstitute/subscriptions","organizations_url":"https://api.github.com/users/broadinstitute/orgs","repos_url":"https://api.github.com/users/broadinstitute/repos","events_url":"https://api.github.com/users/broadinstitute/events{/privacy}","received_events_url":"https://api.github.com/users/broadinstitute/received_events","type":"Organization","site_admin":false},"private":false,"html_url":"https://github.com/broadinstitute/cromwell","description":"Workflow 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