{"action":"created","comment":{"url":"https://api.github.com/repos/ICGC-TCGA-PanCancer/cli/pulls/comments/36908534","id":36908534,"diff_hunk":"@@ -0,0 +1,341 @@\n+#! /usr/bin/python3\n+import json\n+import configparser\n+import time\n+import sys\n+import subprocess\n+import logging\n+from cliff.app import App\n+from cliff.commandmanager import CommandManager\n+from cliff.command import Command\n+\n+class WorkflowLister:\n+    \"Get a listing of workflows from a source of workflow metadata.\"\n+    # Eventually, this data structure should come from some sort of online registry. For now, just define it in code.\n+    _workflows= {   'HelloWorld':\n+                    {\n+                        'full_name':'Workflow_Bundle_HelloWorld_1.0-SNAPSHOT_SeqWare_1.1.1',\n+                        'http_workflow':\n+                        {\n+                            'url':'https://s3.amazonaws.com/oicr.workflow.bundles/released-bundles/Workflow_Bundle_HelloWorld_1.0-SNAPSHOT_SeqWare_1.1.1.zip',\n+                            'version':'1.0-SNAPSHOT'\n+                        },\n+                        'containers':\n+                        {\n+                            'seqware_whitestar_pancancer': {\n+                                'name':'seqware_whitestar_pancancer',\n+                                'image_name': 'pancancer/seqware_whitestar_pancancer:1.1.1'\n+                            }\n+                        },\n+                        'ami_id':'ami-12345',\n+                        'default-ini':'http://something.ini',\n+                        'instance-type':'m3.medium',\n+                        'lvm_devices':'/dev/xvdb,/dev/xvdc,/dev/xvdd,/dev/xvde'\n+                    },\n+                    'Sanger':\n+                    {\n+                        'full_name':'Workflow_Bundle_SangerPancancerCgpCnIndelSnvStr_1.0.8_SeqWare_1.1.0',\n+                        'http_workflow':\n+                        {\n+                            'url':'https://s3.amazonaws.com/oicr.workflow.bundles/released-bundles/Workflow_Bundle_SangerPancancerCgpCnIndelSnvStr_1.0.8_SeqWare_1.1.0.zip',\n+                            'version':'1.0.8'\n+                        },\n+                        'containers':\n+                        {\n+                            'seqware_whitestar_pancancer': {\n+                                'name':'seqware_whitestar_pancancer',\n+                                'image_name': 'pancancer/seqware_whitestar_pancancer:1.1.1'\n+                            }\n+                        },\n+                        'ami_id':'ami-12345',\n+                        'default-ini':'http://something.ini',\n+                        'instance-type':'m3.medium',\n+                        'lvm_devices':'/dev/xvdb,/dev/xvdc,/dev/xvdd,/dev/xvde'\n+                    },\n+                    'BWA':\n+                    {\n+                        'full_name':'Workflow_Bundle_BWA_2.6.5_SeqWare_1.1.1',\n+                        'http_workflow':\n+                        {\n+                            'url':'https://s3.amazonaws.com/oicr.workflow.bundles/released-bundles/Workflow_Bundle_BWA_2.6.5_SeqWare_1.1.1.zip',\n+                            'version':'2.6.5'\n+                        },\n+                        'containers':\n+                        {\n+                            'seqware_whitestar_pancancer': {\n+                                'name':'seqware_whitestar_pancancer',\n+                                'image_name': 'pancancer/seqware_whitestar_pancancer:1.1.1'\n+                            }\n+                        },\n+                        'ami_id':'ami-12345',\n+                        'default-ini':'http://something.ini',\n+                        'instance-type':'m3.medium',\n+                        'lvm_devices':'/dev/xvdb,/dev/xvdc,/dev/xvdd,/dev/xvde'\n+                    },\n+                    'DKFZ_EMBL':\n+                    {\n+                        'full_name':'Workflow_Bundle_DEWrapperWorkflow_1.0.5_SeqWare_1.1.1',\n+                        'http_workflow':\n+                        {\n+                            'url':'https://s3.amazonaws.com/oicr.workflow.bundles/released-bundles/Workflow_Bundle_DEWrapperWorkflow_1.0.5_SeqWare_1.1.1.zip',\n+\n+                            'version':'1.0.5'\n+                        },\n+                        'containers':\n+                        {\n+                            'pcawg-delly-workflow': {\n+                                'name':'pcawg-delly-workflow',\n+                                'image_name': 'pancancer/pcawg-delly-workflow:1.0'\n+                            },\n+                            'seqware_whitestar_pancancer': {\n+                                'name':'seqware_whitestar_pancancer',\n+                                'image_name': 'pancancer/seqware_whitestar_pancancer:1.1.1'\n+                            }\n+                        },\n+                        's3_containers':\n+                        {\n+                            'dkfz_dockered_workflows':\n+                            {\n+                                'name':'dkfz_dockered_workflows',\n+                                'url':'https://s3.amazonaws.com/oicr.docker.private.images/dkfz_dockered_workflows_1.3.tar'\n+                            }\n+                        },\n+                        'ami_id':'ami-12345',\n+                        'default-ini':'http://something.ini',\n+                        'instance-type':'m3.medium',\n+                        'lvm_devices':'/dev/xvdb,/dev/xvdc,/dev/xvdd,/dev/xvde'\n+                    }\n+                }\n+\n+    @staticmethod\n+    def get_workflow_names():\n+        keys = ''\n+        for k in WorkflowLister._workflows:\n+            keys += k+'\\n'\n+        return keys\n+\n+    @staticmethod\n+    def get_workflow_details(workflow_name):\n+        return WorkflowLister._workflows[workflow_name]\n+\n+###\n+\n+class Workflows(Command):\n+    \"This command  can help you configure and select workflows.\"\n+    log = logging.getLogger(__name__)\n+\n+    def get_parser(self,prog_name):\n+        parser = super(Workflows,self).get_parser(prog_name)\n+        #parser.add_mutually_exclusive_group()\n+        workflows_subparser = parser.add_subparsers(title='subcommands',help='workflows subcommands: list and config',dest='subparser_name')\n+        workflows_subparser.add_parser('list',help='Get a list of workflows')\n+        workflows_subparser.add_parser('config',help='Generate a default config file for a specific workflow').add_argument('workflow_name',help='Name of workflow to configure')\n+        return parser\n+\n+    def take_action(self, parsed_args):\n+        subparser_name=vars(parsed_args)['subparser_name']\n+        self.log.debug('subparser: %s',subparser_name)\n+        if subparser_name=='list':\n+            workflow_list = WorkflowLister.get_workflow_names()\n+            print ('Available workflows are:')\n+            print(workflow_list)\n+\n+        elif subparser_name=='config':\n+            workflow_name=vars(parsed_args)['workflow_name']\n+            if workflow_name in WorkflowLister.get_workflow_names():\n+                # TODO: Actually generate the correct INI file!\n+                print('generating default INI in /home/ubuntu/ini-dir/'+workflow_name+'.ini for workflow '+workflow_name)\n+            else:\n+                print ('Sorry, but '+workflow_name+' is not a valid workflow name. Please use the command \\'workflows list\\' to see a list of available workflows.')\n+        else:\n+            print ('The available subcommands are \\'list\\' and \\'config\\'.')","path":"scripts/pancancer.py","position":151,"original_position":151,"commit_id":"17a7de4642bd941bad774ff36cb6435cfb981fdd","original_commit_id":"17a7de4642bd941bad774ff36cb6435cfb981fdd","user":{"login":"niall-byrne","id":9848926,"avatar_url":"https://avatars.githubusercontent.com/u/9848926?v=3","gravatar_id":"","url":"https://api.github.com/users/niall-byrne","html_url":"https://github.com/niall-byrne","followers_url":"https://api.github.com/users/niall-byrne/followers","following_url":"https://api.github.com/users/niall-byrne/following{/other_user}","gists_url":"https://api.github.com/users/niall-byrne/gists{/gist_id}","starred_url":"https://api.github.com/users/niall-byrne/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/niall-byrne/subscriptions","organizations_url":"https://api.github.com/users/niall-byrne/orgs","repos_url":"https://api.github.com/users/niall-byrne/repos","events_url":"https://api.github.com/users/niall-byrne/events{/privacy}","received_events_url":"https://api.github.com/users/niall-byrne/received_events","type":"User","site_admin":false},"body":"Why 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