{"action":"created","issue":{"url":"https://api.github.com/repos/galaxyproject/tools-iuc/issues/239","labels_url":"https://api.github.com/repos/galaxyproject/tools-iuc/issues/239/labels{/name}","comments_url":"https://api.github.com/repos/galaxyproject/tools-iuc/issues/239/comments","events_url":"https://api.github.com/repos/galaxyproject/tools-iuc/issues/239/events","html_url":"https://github.com/galaxyproject/tools-iuc/issues/239","id":98960826,"number":239,"title":"IUC Tools & Collections Hackathon (Fall 2015)","user":{"login":"jmchilton","id":216771,"avatar_url":"https://avatars.githubusercontent.com/u/216771?v=3","gravatar_id":"","url":"https://api.github.com/users/jmchilton","html_url":"https://github.com/jmchilton","followers_url":"https://api.github.com/users/jmchilton/followers","following_url":"https://api.github.com/users/jmchilton/following{/other_user}","gists_url":"https://api.github.com/users/jmchilton/gists{/gist_id}","starred_url":"https://api.github.com/users/jmchilton/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jmchilton/subscriptions","organizations_url":"https://api.github.com/users/jmchilton/orgs","repos_url":"https://api.github.com/users/jmchilton/repos","events_url":"https://api.github.com/users/jmchilton/events{/privacy}","received_events_url":"https://api.github.com/users/jmchilton/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/galaxyproject/tools-iuc/labels/help%20wanted","name":"help wanted","color":"159818"}],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":39,"created_at":"2015-08-04T12:50:37Z","updated_at":"2015-09-25T19:05:48Z","closed_at":null,"body":"We are planning a remote hackathon on **September 17th and 18th** for Galaxy tool developers to work mainly on dataset collections.\r\n\r\nDataset collections enable MapReduce style workflows in Galaxy and have come a long way over the last year+. Several groups are using dataset collections and newer tools to express workflows of various degrees of complexity that were not possible in Galaxy before.\r\n\r\nThe remote nature of this gives people who don't have the opportunity to come to GCC hackathons (which have always been productive and a lot of fun) a chance to participate in a Galaxy hackathon. Having a well defined topic will allow us to accomplish a lot and let people who don't have particular tasks in mind find something to work on very quickly.\r\n\r\nWe are collecting ideas to work on, but we expect to attract the most participation by simply getting tool developers interested in getting help adding collection support to their existing tools and workflows to show up and participate.\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\nThis is the first remote hackathon we have organized and we encourage ideas or advice about how to organize it please let us know. A core group of will be available on IRC all day and we will have 4 google\r\nhangouts across those days to organize, answer questions, and report progress.\r\n\r\n*We 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 (https://github.com/galaxyproject/tools-devteam/issues/26#issuecomment-126957869).\r\n\r\n# Tools to update:\r\n\r\n*Just ideas if these don't make sense remove them*\r\n\r\n- [ ] Tophat2 Readgroups (see galaxyproject/tools-devteam#202)\r\n- [ ] bamtools/samtools split should produce collections ([one](https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/bamtools/bamtools_split/bamtools-split.xml), [two](https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/samtools/samtools_split/samtools_split.xml))\r\n- [ ] fastq_paired_end_deinterlacer\r\n- [ ] fastq_paired_end_interlacer\r\n- [ ] fastq_paired_end_joiner\r\n- [ ] fastq_paired_end_splitter\r\n- [x] Trim Galore\r\n- [ ] Trimmomatic (WIP @ https://github.com/fls-bioinformatics-core/galaxy-tools/tree/trimmomatic-add-dataset-collections)\r\n- [ ] other FASTQ trimmers?\r\n\r\n# New Tools:\r\n\r\n- [ ] Tabular tools (some of this may be covered by unix tools) \r\n   - [ ] concatenate rows together and add columns for collection identifiers\r\n   - [ ] concatenate columns to a table for each element in a collection (ever a use for this?)\r\n   - [x] Split out a table based on unique values in column (1 table -> collection of tables) [split_file_on_column.xml](https://github.com/bgruening/galaxytools/blob/master/tools/text_processing/split_file_on_column/split_file_on_column.xml) \r\n- [ ] Tool for concatenating plain textual data (ignoring identifiers I guess)\r\n- [ ] Create a tool that takes in a bam file and produces collection of regions (bed files).\r\n  - [ ] Document a simple workflow that uses this to parallelize work over a bam file in a workflow.\r\n- [ ] Ensure we have sufficient coverage to merge/reduce various other formats.\r\n  - [ ] bam/sam\r\n  - [ ] ...\r\n\r\n# general updates\r\n- [x] Replace `<repeats>` where needed with `multiple=\"True\"` in\r\n  - [x] `tools-iuc`\r\n  - [x] `tools-devteam`\r\n  - [x] `galaxytools`\r\n- [ ] migrate the text manipulation tools ([unix-tools](https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing)) to perform reduce steps\r\n\r\n# Documentation:\r\n\r\n- [ ] Update planemo collection documentation to include information on creating tools that output collections. Add planemo docs for [BB PR #634](https://bitbucket.org/galaxy/galaxy-central/pull-requests/634/allow-tools-to-explicitly-produce-dataset/diff) and [Git PR #538](https://github.com/galaxyproject/galaxy/pull/538).\r\n- [ ] Document using regions to parallelize work over a bam file in a workflow as a tip in planemo docs.\r\n- [ ] Document using read group macros and general techniques for dealing with read groups in a collection aware fashion in planemo docs. Potentially based off [tools-devteam #103](https://github.com/galaxyproject/tools-devteam/pull/103).\r\n- [ ] Add visual descriptions of various map & reduce operations to planemo documentation.\r\n- [ ] Add end user documentation for using collections in tools. Histories has nice documentation [here](https://wiki.galaxyproject.org/Histories), but I don't think similar documentation exists for tools.\r\n"},"comment":{"url":"https://api.github.com/repos/galaxyproject/tools-iuc/issues/comments/143324838","html_url":"https://github.com/galaxyproject/tools-iuc/issues/239#issuecomment-143324838","issue_url":"https://api.github.com/repos/galaxyproject/tools-iuc/issues/239","id":143324838,"user":{"login":"Public-Health-Bioinformatics","id":10779910,"avatar_url":"https://avatars.githubusercontent.com/u/10779910?v=3","gravatar_id":"","url":"https://api.github.com/users/Public-Health-Bioinformatics","html_url":"https://github.com/Public-Health-Bioinformatics","followers_url":"https://api.github.com/users/Public-Health-Bioinformatics/followers","following_url":"https://api.github.com/users/Public-Health-Bioinformatics/following{/other_user}","gists_url":"https://api.github.com/users/Public-Health-Bioinformatics/gists{/gist_id}","starred_url":"https://api.github.com/users/Public-Health-Bioinformatics/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Public-Health-Bioinformatics/subscriptions","organizations_url":"https://api.github.com/users/Public-Health-Bioinformatics/orgs","repos_url":"https://api.github.com/users/Public-Health-Bioinformatics/repos","events_url":"https://api.github.com/users/Public-Health-Bioinformatics/events{/privacy}","received_events_url":"https://api.github.com/users/Public-Health-Bioinformatics/received_events","type":"User","site_admin":false},"created_at":"2015-09-25T19:05:48Z","updated_at":"2015-09-25T19:05:48Z","body":"@erasche You mentioned \"advanced exit code detection routines in galaxy.\"  I would like more info on that.  My QC tool basically lets one set up rules that trigger whether to stop a job or continue, as well as reporting on QC metrics.  I'm now at the point where I need to code the stop a job part.  Assuming its just a matter of exit code 1, but if you folks have some new options or things to understand I'd like to learn.\r\n\r\nThanks,\r\n\r\nDamion"}}