Mercurial > repos > yating-l > hubarchivecreator_test
comparison hub-archive-creator/README.md @ 6:9193fe3ee73f draft default tip
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| author | yating-l |
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| date | Thu, 22 Dec 2016 15:59:24 -0500 |
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| 5:48d7b2dddae6 | 6:9193fe3ee73f |
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| 1 # Hub Archive Creator | |
| 2 This Galaxy tool permits to prepare your files to be ready for Assembly Hub visualization. | |
| 3 | |
| 4 Into a publicly accessible Galaxy (Linux for maximum tools compatibility), you will be able to use UCSC Genome Browser fonctionality to see your tracks. | |
| 5 | |
| 6 ## Features | |
| 7 1. Create a structure for your tracks, and convert them to more efficient datatypes (e.g Bed => BigBed) | |
| 8 2. Benefits from Galaxy strong features as well as UCSC Genome Browser's ones without the hassle to move your data from one to another | |
| 9 3. Download and store, as a zip file, your tracks structured for UCSC TrackHub use | |
| 10 4. Create workflows within Galaxy to automatize pipeline analysis and get them ready to visualization inside UCSC Genome Browser...in a few clicks! | |
| 11 | |
| 12 At the moment, Supported datatypes are: | |
| 13 - Bam | |
| 14 - Bed (Generic and Simple Repeats) | |
| 15 - BigWig | |
| 16 - Gff3 | |
| 17 - Gtf | |
| 18 - Psl | |
| 19 | |
| 20 ## Installation: | |
| 21 1. You would need to add this tool into your Galaxy. | |
| 22 1. (strongly preferred) **ToolShed Installation**: Tool is in [toolshed](https://toolshed.g2.bx.psu.edu/view/rmarenco/hubarchivecreator/fb5e60d4d18a) | |
| 23 2. OR **Local Installation**: See https://wiki.galaxyproject.org/Admin/Tools/AddToolTutorial | |
| 24 2. The tool can be used with or without Conda (activate it in your galaxy.ini) | |
| 25 3. If installed without TS (by downloading on GitHub), you need to have all the binaries accessible within Galaxy. | |
| 26 You can use the script [install_linux_binaries](util/install_linux_binaries) with a linux x86-64 (64bits) | |
| 27 4. Install the UCSC Track Hub datatype: | |
| 28 1. **Easy** => Use Galaxy 16.07 or latest to directly have Track Hub Datatype (See [this Galaxy Pull Request](https://github.com/galaxyproject/galaxy/pull/2348) for more information) | |
| 29 2. OR Look into [trackHub README](trackHub/README.md) for more information or if you want to use Galaxy < 16.07 | |
| 30 | |
| 31 ### Binaries used by HAC: | |
| 32 - bedToBigBed | |
| 33 - faToTwoBit | |
| 34 - genePredToBed | |
| 35 - genePredToBigGenePred | |
| 36 - gff3ToGenePred | |
| 37 - gtfToGenePred | |
| 38 - pslToBigPsl | |
| 39 - samtools | |
| 40 - sort | |
| 41 - twoBitInfo | |
| 42 See `<requirements` in [tool_dependencies.xml](tool_dependencies.xml) for an up-to-date used binaries list | |
| 43 | |
| 44 ## Future | |
| 45 See [TODO.md](todo.md) for more information | |
| 46 | |
| 47 ## Contribute | |
| 48 | |
| 49 - Issue Tracker: https://github.com/remimarenco/hub-archive-creator/issues | |
| 50 - Source Code: https://github.com/remimarenco/hub-archive-creator | |
| 51 | |
| 52 ## Support | |
| 53 | |
| 54 If you are having issues, please let us know. | |
| 55 | |
| 56 - For more information about how to use G-OnRamp: | |
| 57 - [Wilson Leung](wleung@wustl.edu) - Product owner and developer | |
| 58 - [Yating Liu](yliu41@wustl.edu) - Community manager and Developer | |
| 59 - [Remi Marenco](remimarenco@gmail.com) - Main developer and Scrum Master | |
| 60 | |
| 61 - For more information about the project vision, or for partneship: | |
| 62 - [Elgin, Sarah](selgin@wustl.edu) - PI | |
| 63 - [Jeremy Goecks](jgoecks@gwu.edu) - PI | |
| 64 | |
| 65 ## License | |
| 66 | |
| 67 The project is licensed under the Academic Free License 3.0. See [LICENSE.txt](LICENSE.txt). |