ruby-igv

Installation

Requirement: IGV (Integrative Genomics Viewer) and Ruby.

gem install ruby-igv

Usage

Enable IGV to listen on the port: Preference > Advanced > Enable port

igv = IGV.new
igv.genome 'hg19'
igv.load   'http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqK562G1AlnRep1.bam'
igv.go     'chr18:78,016,233-78,016,640'
igv.save   '/tmp/r/region.svg'
igv.save   '/tmp/r/region.png'
igv.snapshot_dir = '/tmp/r2/'
igv.save   'region.jpg'  # save to /tmp/r2/region.png
igv.send   'echo'        # whatever you want

See the list of Batch commands.

Contributing

• Report bugs
• Fix bugs and submit pull requests
• Write, clarify, or fix documentation
• Suggest or add new features

Do you need commit rights to my repository?
Do you want to get admin rights and take over the project?
If so, please feel free to contact me @kojix2.

Acknowledgement

This gem is strongly inspired by a Python script developed by Brent Pedersen.

• brentp/bio-playground/igv.

License

The gem is available as open source under the terms of the MIT License.