dirHub

A trackHub configurator with directory structure projection.

dirHub is a tool to assist configuration of trackHub by mapping a directory structure of data files to a layer of tracks. Check demo server on Heroku

Note this is still under development (alpha ver.)

Supported file type

• bigBed (.bb)
• bigWig (.bw)
• superTrack (.st)
• composite track (.cp)
• multWig (.mw)

Usage (web application)

installation

$ git clone https://github.com/hkawaji/dirHub.git 
$ cd dirHub
$ bundle install --path vendor/bundle

launch the web application

$ bundle exec ruby dirHub.rb --webapp

Now you are ready to access the web interface, for example http://YOURHOST:4567

Usage (command line tool)

installation

$ git clone https://github.com/hkawaji/dirHub.git 
$ cd dirHub

basic usage

$ cd ${DATA_DIR}
$ ${PROGRAM_DIR}/dirHub.rb --input-trackfiles=. --output-config-dir=.

help message

$ ${PROGRAM_DIR}/dirHub.rb --help

Requirements

• ruby (tested in version 2.3)

To set up trackHub for your own purpose, you also need:

• trackHub compatible genome browser (tested on the UCSC Genome Browser / trackHub definition v2)
• a web serpver hosting the data files

Reference

• Kawaji H. "dirHub: a trackHub configurator with directory structure projection", bioRxiv 314807, doi: https://doi.org/10.1101/314807

Author, copyright, and license

This software is written by Hideya Kawaji. Copyright (c) 2018 RIKEN. Distributed under Apache License 2.0.