{"action":"created","issue":{"url":"https://api.github.com/repos/maximilianh/crisporWebsite/issues/16","repository_url":"https://api.github.com/repos/maximilianh/crisporWebsite","labels_url":"https://api.github.com/repos/maximilianh/crisporWebsite/issues/16/labels{/name}","comments_url":"https://api.github.com/repos/maximilianh/crisporWebsite/issues/16/comments","events_url":"https://api.github.com/repos/maximilianh/crisporWebsite/issues/16/events","html_url":"https://github.com/maximilianh/crisporWebsite/issues/16","id":361218058,"node_id":"MDU6SXNzdWUzNjEyMTgwNTg=","number":16,"title":"a few suggestions to facilitate local installation and execution","user":{"login":"loire","id":3297393,"node_id":"MDQ6VXNlcjMyOTczOTM=","avatar_url":"https://avatars0.githubusercontent.com/u/3297393?v=4","gravatar_id":"","url":"https://api.github.com/users/loire","html_url":"https://github.com/loire","followers_url":"https://api.github.com/users/loire/followers","following_url":"https://api.github.com/users/loire/following{/other_user}","gists_url":"https://api.github.com/users/loire/gists{/gist_id}","starred_url":"https://api.github.com/users/loire/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/loire/subscriptions","organizations_url":"https://api.github.com/users/loire/orgs","repos_url":"https://api.github.com/users/loire/repos","events_url":"https://api.github.com/users/loire/events{/privacy}","received_events_url":"https://api.github.com/users/loire/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":10,"created_at":"2018-09-18T09:37:00Z","updated_at":"2018-09-19T09:14:26Z","closed_at":null,"author_association":"NONE","body":"Hi, \r\nI'm currently using crispor, thanks for sharing the code. \r\n\r\nI cloned the repo the 17 septembre 2018 (commit  2d08207)\r\n\r\nI ran through a few hurdles during installation/execution (despite a nice README) which I overcame this way:\r\nI used a virtual environment with python 2.7.7, it helped to install the correct versions of the dependencies. \r\nBut it can broke the execution of some of the utils tools because of inconsistencies between python 3 (default on my system) and the virtual 2.7 \r\nUsing #!usr/bin/env python as shebang in all scripts saved the day. I think you could replace them systematically.\r\n\r\nBedBetween and bedOverlaperge raised an indentation error, I corrected them in my editor.\r\n\r\nin crisprAddGenome, line 991, before invoking ./makeGenomeInfo, the script tries to cd in \"/data/www/crispor\" which is not necessarly an existing path nor the correct one depending on where the script is stored. \r\nHope it helps :)\r\n\r\nThanks again, will let you know how it runs \r\n \r\n\r\n\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/maximilianh/crisporWebsite/issues/comments/422721948","html_url":"https://github.com/maximilianh/crisporWebsite/issues/16#issuecomment-422721948","issue_url":"https://api.github.com/repos/maximilianh/crisporWebsite/issues/16","id":422721948,"node_id":"MDEyOklzc3VlQ29tbWVudDQyMjcyMTk0OA==","user":{"login":"maximilianh","id":310861,"node_id":"MDQ6VXNlcjMxMDg2MQ==","avatar_url":"https://avatars1.githubusercontent.com/u/310861?v=4","gravatar_id":"","url":"https://api.github.com/users/maximilianh","html_url":"https://github.com/maximilianh","followers_url":"https://api.github.com/users/maximilianh/followers","following_url":"https://api.github.com/users/maximilianh/following{/other_user}","gists_url":"https://api.github.com/users/maximilianh/gists{/gist_id}","starred_url":"https://api.github.com/users/maximilianh/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/maximilianh/subscriptions","organizations_url":"https://api.github.com/users/maximilianh/orgs","repos_url":"https://api.github.com/users/maximilianh/repos","events_url":"https://api.github.com/users/maximilianh/events{/privacy}","received_events_url":"https://api.github.com/users/maximilianh/received_events","type":"User","site_admin":false},"created_at":"2018-09-19T09:14:26Z","updated_at":"2018-09-19T09:14:26Z","author_association":"OWNER","body":"Would you be able to share the input sequence region?\n\nI've used crispor on big input regions before, we use it for the whole\ngenome at UCSC. So it's working in principle, but it's possible that I\nmodified something with the repeat filtering that broke it recently.\n\nOn Wed, Sep 19, 2018 at 4:08 AM, etienne loire <notifications@github.com>\nwrote:\n\n> I may use a combination of both: Flashfry was able to process the 300kb\n> chunk easily, got more 20,000 potential guide that I will filter according\n> to my colleagues preference, then use crispor to get the neat additional\n> infos on the locus.\n> Fyi, samToBed is still running 10hours later, I think it was the culprit\n> for the broken pipe.\n>\n> You may close the issue: My main problem was that crispor is unfortunately\n> unsuitable for such a large genomic segment !\n> Cheers\n> E.\n>\n> —\n> You are receiving this because you commented.\n> Reply to this email directly, view it on GitHub\n> <https://github.com/maximilianh/crisporWebsite/issues/16#issuecomment-422701476>,\n> or mute the thread\n> <https://github.com/notifications/unsubscribe-auth/AAS-TWO8y0C3lTFNMFpDApen3JRwpNA-ks5ucft6gaJpZM4WtiL->\n> .\n>\n"}}
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