{"action":"created","issue":{"url":"https://api.github.com/repos/koszullab/GRAAL/issues/1","labels_url":"https://api.github.com/repos/koszullab/GRAAL/issues/1/labels{/name}","comments_url":"https://api.github.com/repos/koszullab/GRAAL/issues/1/comments","events_url":"https://api.github.com/repos/koszullab/GRAAL/issues/1/events","html_url":"https://github.com/koszullab/GRAAL/issues/1","id":85433276,"number":1,"title":"Documentation is insufficient to get this software running.","user":{"login":"cerebis","id":6006667,"avatar_url":"https://avatars.githubusercontent.com/u/6006667?v=3","gravatar_id":"","url":"https://api.github.com/users/cerebis","html_url":"https://github.com/cerebis","followers_url":"https://api.github.com/users/cerebis/followers","following_url":"https://api.github.com/users/cerebis/following{/other_user}","gists_url":"https://api.github.com/users/cerebis/gists{/gist_id}","starred_url":"https://api.github.com/users/cerebis/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cerebis/subscriptions","organizations_url":"https://api.github.com/users/cerebis/orgs","repos_url":"https://api.github.com/users/cerebis/repos","events_url":"https://api.github.com/users/cerebis/events{/privacy}","received_events_url":"https://api.github.com/users/cerebis/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2015-06-05T05:25:02Z","updated_at":"2015-09-09T22:58:44Z","closed_at":null,"body":"The documentation you have provided is  incomplete. \r\n\r\nThe README refers to data files, which I assume are examples, but these are no where to be found either in Github or your papers supplementary data.\r\n\r\nWhen I try to run this program using my own fasta sequences, I get the following error when hitting \"build\" after selecting a fasta file:\r\n```bash\r\nTraceback (most recent call last):\r\n  File \"main_window.py\", line 353, in OnReturn\r\n    self.main_window.pyramid = self.pyramid\r\nAttributeError: 'LoaderWindow' object has no attribute 'pyramid'\r\nException in thread Thread-1:\r\nTraceback (most recent call last):\r\n  File \"/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/threading.py\", line 810, in __bootstrap_inner\r\n    self.run()\r\n  File \"main_window.py\", line 89, in run\r\n    pyramid = pyr.build_and_filter(self.base_folder, self.size_pyramid, self.factor)\r\n  File \"/Users/foobar/git/GRAAL/pyramid_sparse.py\", line 36, in build_and_filter\r\n    build(base_folder, init_size_pyramid, factor, min_bin_per_contig,)\r\n  File \"/Users/foobar/git/GRAAL/pyramid_sparse.py\", line 168, in build\r\n    shutil.copyfile(contig_info,current_contig_info)\r\n  File \"/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/shutil.py\", line 82, in copyfile\r\n    with open(src, 'rb') as fsrc:\r\nIOError: [Errno 2] No such file or directory: u'/Users/foobar/git/GRAAL/workdir/info_contigs.txt'\r\n```\r\nYour code is trying to copy a file that doesn't yet exist. If this is some sort of guide file that I need to create beforehand, it's necessary to tell me what goes into it and where to put it. Perhaps this is a hanging legacy of development, where you've always had this dependency satisfied but were unaware that it existed.\r\n\r\nAm I also only guessing what sequences are meant to be selected at this point. Is it the contigs? I would have a better idea if the next window was available, but GRAAL won't open until the pyramid is created.\r\n\r\nSo, please specify the file formats for:\r\n- info_contigs.txt\r\n- abs_fragments_contacts_weighted.txt\r\n\r\nOr explain how these can be satisfied, as I cannot get passed this step."},"comment":{"url":"https://api.github.com/repos/koszullab/GRAAL/issues/comments/139067336","html_url":"https://github.com/koszullab/GRAAL/issues/1#issuecomment-139067336","issue_url":"https://api.github.com/repos/koszullab/GRAAL/issues/1","id":139067336,"user":{"login":"MacCampbell","id":6517923,"avatar_url":"https://avatars.githubusercontent.com/u/6517923?v=3","gravatar_id":"","url":"https://api.github.com/users/MacCampbell","html_url":"https://github.com/MacCampbell","followers_url":"https://api.github.com/users/MacCampbell/followers","following_url":"https://api.github.com/users/MacCampbell/following{/other_user}","gists_url":"https://api.github.com/users/MacCampbell/gists{/gist_id}","starred_url":"https://api.github.com/users/MacCampbell/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/MacCampbell/subscriptions","organizations_url":"https://api.github.com/users/MacCampbell/orgs","repos_url":"https://api.github.com/users/MacCampbell/repos","events_url":"https://api.github.com/users/MacCampbell/events{/privacy}","received_events_url":"https://api.github.com/users/MacCampbell/received_events","type":"User","site_admin":false},"created_at":"2015-09-09T22:58:44Z","updated_at":"2015-09-09T22:58:44Z","body":"Hi,\r\n\r\nYes, the documentation is incomplete.\r\n\r\nAre you still trying to get it to work? I can provide some omitted scripts and these files:\r\n\r\n    info_contigs.txt\r\n    abs_fragments_contacts_weighted.txt\r\n\r\nI'm in the process of trying to get it work myself. Perhaps we should fork it? Though, I'm a long way from getting a test data set off the ground.\r\n\r\n\r\n\r\n\r\n"}}