Mercurial > repos > rmarenco > hub_archive_creator
comparison hub-archive-creator-1.6/README.md @ 0:163b2de763ea draft
Upload the full hubArchiveCreator archive
| author | rmarenco |
|---|---|
| date | Tue, 01 Mar 2016 19:43:25 -0500 |
| parents | |
| children |
comparison
equal
deleted
inserted
replaced
| -1:000000000000 | 0:163b2de763ea |
|---|---|
| 1 # Hub Archive Creator | |
| 2 This Galaxy tool permits to prepare your files to be ready for Assembly Hub visualization. | |
| 3 | |
| 4 To try the software, you need to have a .gff3 and a .fa as input and set an output filename: | |
| 5 ```hubArchiveCreator.py -g test_data/augustusDbia3.gff3 -f test_data/dbia3.fa -o output.zip``` | |
| 6 | |
| 7 You will get a .zip file, that you need to put on a server accessible from the outside. Then use UCSC track hubs fonctionality to see your track. | |
| 8 | |
| 9 ## Requirements: | |
| 10 1. You need to install [Mako](http://www.makotemplates.org/download.html) | |
| 11 2. HubArchiveCreator use, for now, tools from UCSC Kent Utils. This repository use the linux.x86_64/ ones, but you NEED to replace them accordingly to your architecture. | |
| 12 Here is the link to get these tools: http://hgdownload.soe.ucsc.edu/admin/exe/ | |
| 13 | |
| 14 ### Install in Galaxy | |
| 15 1. Take the hubAssembly.py in the hubaDatatype folder, and add it into lib/galaxy/datatypes in your Galaxy instance | |
| 16 2. Add this line in config/datatypes_conf.xml: | |
| 17 ```<datatype extension="huba" type="galaxy.datatypes.hubAssembly:HubAssembly" display_in_upload="true" />``` | |
| 18 3. Look into hubaDatatype/README.md for more informations |