{"action":"created","issue":{"url":"https://api.github.com/repos/galaxyproject/tools-iuc/issues/422","labels_url":"https://api.github.com/repos/galaxyproject/tools-iuc/issues/422/labels{/name}","comments_url":"https://api.github.com/repos/galaxyproject/tools-iuc/issues/422/comments","events_url":"https://api.github.com/repos/galaxyproject/tools-iuc/issues/422/events","html_url":"https://github.com/galaxyproject/tools-iuc/issues/422","id":119246188,"number":422,"title":"IUC Contribution Fest - RADSeq Tools and Workflows","user":{"login":"tiagoantao","id":34787,"avatar_url":"https://avatars.githubusercontent.com/u/34787?v=3","gravatar_id":"","url":"https://api.github.com/users/tiagoantao","html_url":"https://github.com/tiagoantao","followers_url":"https://api.github.com/users/tiagoantao/followers","following_url":"https://api.github.com/users/tiagoantao/following{/other_user}","gists_url":"https://api.github.com/users/tiagoantao/gists{/gist_id}","starred_url":"https://api.github.com/users/tiagoantao/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tiagoantao/subscriptions","organizations_url":"https://api.github.com/users/tiagoantao/orgs","repos_url":"https://api.github.com/users/tiagoantao/repos","events_url":"https://api.github.com/users/tiagoantao/events{/privacy}","received_events_url":"https://api.github.com/users/tiagoantao/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":4,"created_at":"2015-11-27T21:07:16Z","updated_at":"2015-12-01T19:17:59Z","closed_at":null,"body":"We are planning a Remote Contribution Fest on **7th and 8th of March** for developers to work on Galaxy RADSeq tools.\r\n\r\nRADSeq is a cheap sequencing technology that is used by many resource-limited groups who would benefit a lot from easy-to-use galaxy tools. Indeed there has been quite some interest in analyzing RADSeq with Galaxy. Currently there is a wrapper for stacks and little more to help with RAD specific analysis (though many other galaxy tools are useful with RADs - bwa, cap3, gatk, velvet, ...).\r\n\r\nIf you are interested in participating in the hackathon but not interested in actual tool development - we will assemble a list of smaller, manageable Python and JavaScript tasks to work on and certainly documentation is a chronically lacking for collections so we could use help there and no actual coding would be required.\r\n\r\nWe encourage ideas or advice about how to organize this so please let us know. A core group will be available on IRC all day and we will have google hangouts across those days to organize, answer questions, and report progress.\r\n\r\nWe will do our best to coordinate and make this hackathon a nice and productive experience and we would like to especially focus on working reasonable hours and discourage overnighters.\r\n\r\n**All forms of contribution are welcome!**\r\n\r\nOriginal idea from @bgruening (galaxyproject/tools-devteam#26 (comment)). See #299 and #239 for information on the last two hackathons. This text is inspired on #299.\r\n\r\n## Things to work on\r\n\r\nThis list will be updated as comments are made on the issue. Your are strongly encouraged to leave your suggestion/opinion/criticism below.\r\n\r\nNote that while the list is currently stacks-oriented, there is no reason for that to be the final list of stuff to do... **Non-stacks based suggestions are strongly encouraged**\r\n\r\n* Existing stacks plugin\r\n  * Support for data collections\r\n  * cap3 integration\r\n  * support multi-threading (GALAXY_SLOTS)\r\n  * upgrade the version of stacks\r\n  * support clone_filter\r\n* Implement stacks workflows\r\n* Check the feasibility of implementing the stacks web interface on Galaxy\r\n* have a process_radtags alike with a configurable enzyme sequence (i.e allow demultiplexing using a configurable sequence)\r\n* [PyRAD](https://github.com/dereneaton/pyrad)\r\n* [dDocent](https://github.com/jpuritz/dDocent) \r\n\r\n## Reading list\r\n\r\n* [Stacks homepage](http://catchenlab.life.illinois.edu/stacks/)\r\n* [Population Genomics of Parallel Adaptation in Threespine Stickleback using Sequenced RAD Tags] (http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1000862)\r\n* [Analyse de données RADseq sous Galaxy : l'exemple de STACKS](https://www.e-biogenouest.org/resources/1321) - In French from @yvanlebras\r\n* [PyRAD documentation](http://nbviewer.ipython.org/gist/dereneaton/af9548ea0e94bff99aa0/pyRAD_v.3.0.ipynb) - Jupyter notebook"},"comment":{"url":"https://api.github.com/repos/galaxyproject/tools-iuc/issues/comments/161067684","html_url":"https://github.com/galaxyproject/tools-iuc/issues/422#issuecomment-161067684","issue_url":"https://api.github.com/repos/galaxyproject/tools-iuc/issues/422","id":161067684,"user":{"login":"tiagoantao","id":34787,"avatar_url":"https://avatars.githubusercontent.com/u/34787?v=3","gravatar_id":"","url":"https://api.github.com/users/tiagoantao","html_url":"https://github.com/tiagoantao","followers_url":"https://api.github.com/users/tiagoantao/followers","following_url":"https://api.github.com/users/tiagoantao/following{/other_user}","gists_url":"https://api.github.com/users/tiagoantao/gists{/gist_id}","starred_url":"https://api.github.com/users/tiagoantao/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tiagoantao/subscriptions","organizations_url":"https://api.github.com/users/tiagoantao/orgs","repos_url":"https://api.github.com/users/tiagoantao/repos","events_url":"https://api.github.com/users/tiagoantao/events{/privacy}","received_events_url":"https://api.github.com/users/tiagoantao/received_events","type":"User","site_admin":false},"created_at":"2015-12-01T19:17:59Z","updated_at":"2015-12-01T19:17:59Z","body":"@bgruening @abretaud I have added a link to PyRad documentation. I will probably send an email to the author to see if he wants to participate. He is a Python programmer, so he might be interested..."}}