{"action":"created","issue":{"url":"https://api.github.com/repos/choderalab/ensembler/issues/47","labels_url":"https://api.github.com/repos/choderalab/ensembler/issues/47/labels{/name}","comments_url":"https://api.github.com/repos/choderalab/ensembler/issues/47/comments","events_url":"https://api.github.com/repos/choderalab/ensembler/issues/47/events","html_url":"https://github.com/choderalab/ensembler/issues/47","id":102846000,"number":47,"title":"ensembler installation","user":{"login":"mihirdate","id":5077103,"avatar_url":"https://avatars.githubusercontent.com/u/5077103?v=3","gravatar_id":"","url":"https://api.github.com/users/mihirdate","html_url":"https://github.com/mihirdate","followers_url":"https://api.github.com/users/mihirdate/followers","following_url":"https://api.github.com/users/mihirdate/following{/other_user}","gists_url":"https://api.github.com/users/mihirdate/gists{/gist_id}","starred_url":"https://api.github.com/users/mihirdate/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mihirdate/subscriptions","organizations_url":"https://api.github.com/users/mihirdate/orgs","repos_url":"https://api.github.com/users/mihirdate/repos","events_url":"https://api.github.com/users/mihirdate/events{/privacy}","received_events_url":"https://api.github.com/users/mihirdate/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":5,"created_at":"2015-08-24T17:10:21Z","updated_at":"2015-08-26T02:45:18Z","closed_at":null,"body":"Hi guys,\r\nI am trying to install ensembler. We installed anaconda as one of the modules on or system and then followed ensembler installation steps using conda config. Now, ensembler --help displays help menu of ensembler. \r\nBut when I tried running ensembler example as follows,   \r\n\r\n$ensembler quickmodel --target_uniprot_entry_name EGFR_HUMAN --uniprot_domain_regex '^Protein kinase' --template_pdbids 4KB8 --no-loopmodel\r\n\r\nFollowing is the output I get.\r\n\r\n#########################output ###########################\r\nTraceback (most recent call last):\r\n  File \"/opt/az/local/anaconda/2.3.0/installdir/bin/ensembler\", line 6, in <module>\r\n    sys.exit(main())\r\n  File \"/opt/az/local/anaconda/2.3.0/installdir/lib/python2.7/site-packages/ensembler/cli.py\", line 40, in main\r\n    command.dispatch(args)\r\n  File \"/opt/az/local/anaconda/2.3.0/installdir/lib/python2.7/site-packages/ensembler/cli_commands/quickmodel.py\", line 106, in dispatch\r\n    QuickModel(targetid=args['--targetid'], templateids=templateids, target_uniprot_entry_name=args['--target_uniprot_entry_name'], uniprot_domain_regex=args['--uniprot_domain_regex'], pdbids=pdbids, chainids=chainids_dict, template_uniprot_query=args['--template_uniprot_query'], template_seqid_cutoff=template_seqid_cutoff, loopmodel=not args['--no-loopmodel'], package_for_fah=args['--package_for_fah'], nfahclones=nfahclones, structure_dirs=structure_paths)\r\n  File \"/opt/az/local/anaconda/2.3.0/installdir/lib/python2.7/site-packages/ensembler/tools/quick_model.py\", line 58, in __init__\r\n    gather_targets_obj = ensembler.initproject.GatherTargetsFromUniProt(uniprot_query_string, uniprot_domain_regex=self.uniprot_domain_regex)\r\n  File \"/opt/az/local/anaconda/2.3.0/installdir/lib/python2.7/site-packages/ensembler/initproject.py\", line 181, in __init__\r\n    super(GatherTargetsFromUniProt, self).__init__()\r\n  File \"/opt/az/local/anaconda/2.3.0/installdir/lib/python2.7/site-packages/ensembler/initproject.py\", line 90, in __init__\r\n    self.manual_overrides = ensembler.core.ManualOverrides()\r\n  File \"/opt/az/local/anaconda/2.3.0/installdir/lib/python2.7/site-packages/ensembler/core.py\", line 257, in __init__\r\n    self.target = TargetManualOverrides(manual_overrides_yaml)\r\n  File \"/opt/az/local/anaconda/2.3.0/installdir/lib/python2.7/site-packages/ensembler/core.py\", line 275, in __init__\r\n    target_dict = manual_overrides_yaml.get('target-selection')\r\nAttributeError: 'NoneType' object has no attribute 'get'\r\n\r\n####################################\r\n\r\nCan anyone tell if this is installation issue or usage?\r\n\r\nBest,\r\nMihir"},"comment":{"url":"https://api.github.com/repos/choderalab/ensembler/issues/comments/134798722","html_url":"https://github.com/choderalab/ensembler/issues/47#issuecomment-134798722","issue_url":"https://api.github.com/repos/choderalab/ensembler/issues/47","id":134798722,"user":{"login":"jchodera","id":3656088,"avatar_url":"https://avatars.githubusercontent.com/u/3656088?v=3","gravatar_id":"","url":"https://api.github.com/users/jchodera","html_url":"https://github.com/jchodera","followers_url":"https://api.github.com/users/jchodera/followers","following_url":"https://api.github.com/users/jchodera/following{/other_user}","gists_url":"https://api.github.com/users/jchodera/gists{/gist_id}","starred_url":"https://api.github.com/users/jchodera/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jchodera/subscriptions","organizations_url":"https://api.github.com/users/jchodera/orgs","repos_url":"https://api.github.com/users/jchodera/repos","events_url":"https://api.github.com/users/jchodera/events{/privacy}","received_events_url":"https://api.github.com/users/jchodera/received_events","type":"User","site_admin":false},"created_at":"2015-08-26T02:45:18Z","updated_at":"2015-08-26T02:45:18Z","body":"This error looks like it can't get to the RCSB or UniProt via HTTP.\r\n\r\nDo you guys have some sort of proxy you need to use to access standard websites like the RCSB or UniProt?\r\n\r\nHave you tried this from, say, the MSKCC hal cluster?"}}