How to embed genome browser in a web site?

Question

[biolab]

Dear All,

I am asking you for the ways of embedding genome browser on a web site, so as to visualize genome easily by others. I tried to install GBrowser, but failed with many errors. The apache is successfully install. Do you know alternative tools for this job? Thank you very much!

[Pierre Lindenbaum]

. I tried to install GBrowser, but failed with many errors.

did you try to get help from GBrowser's authors ?

[Michael]

The software is called GBrowse, [e-mail] is the mailing list to get support. You should provide the exact error messages and commands used in your attempt to install it. There are alternative tools, but they are not necessarily easier to install.

Answer 1

[Jean-Karim Heriche]

Have a look at Genoverse.

[biolab]

Thank you all for your comments and answers!

Answer 2

[cmdcolin]

JBrowse may be somewhat easier than GBrowse. The general idea behind setting up jbrowse is

• just download the zip file from jbrowse.org, e.g. https://jbrowse.org/releases/JBrowse-1.12.1.zip
• unzip this file into your normal web folder like /var/www/html or similar, so that you have /var/www/html/jbrowse
• you should probably make this file "owned" by you e.g. sudo chown -R myusername /var/www/html/jbrowse just so you don't have to use sudo a lot (not strictly necessary)
• now cd into /var/www/html/jbrowse and run the setup.sh script e.g. ./setup.sh. as long as it completes the "Installing Perl pre-requisites" phase of setup.sh you should be good to go (the other steps are not strictly needed)
• open up your website e.g. http://localhost/jbrowse and you'll already see that is is "setup" and you can see http://localhost/jbrowse/?data=sample_data/json/volvox has example data

You are now 90% of the way there. Then you can simply run a small script to get your own genome loaded. For example, while you are in /var/www/html/jbrowse folder, then run

bin/prepare-refseqs.pl --fasta your_genome.fa

This will create a folder named "data" and then visiting http://localhost/jbrowse/ will automatically look in this folder and show you your data

See http://jbrowse.org/code/JBrowse-1.12.1/docs/tutorial/ and the "JBrowse Configuration Guide" http://gmod.org/wiki/JBrowse_Configuration_Guide for more. Note that JBrowse does not use any "backend" scripts such as PHP, Perl-CGI, or databases like Mysql, which makes this setup much easier and more self contained (you can in fact think of jbrowse as a "static site generator" like jekyll)

Email [e-mail] or visit github https://github.com/gmod/jbrowse for support

[biolab]

Hi, cmdcolin, Thanks a lot for your detailed answer! Now I have installed JBrowse and am able to view the volvox example. When trying my own data, I encounter a problem. I used the following commands to view genome and GFF tracks. sudo perl bin/prepare-refseqs.pl --fasta genome.fa --out data and sudo perl bin/flatfile-to-json.pl --gff genome.gff --trackLabel TAIR --key TAIR --type mRNA,exon,CDS --out data. I could see the genome fasta on JBrowse, but could not see the gene structure information provided by the GFF file. Did I use the correct command to input the GFF track? Thanks!

[cmdcolin]

Hi biolab, sorry I did not get notified that you responded to my post. You command look basically correct. Did you end up getting it solved yourself yet? Do you have a screenshot of what it looks like in your browser? If the track is in the tracklist sidebar, but the features are not showing up in the track, then this often means that the "chromosome names" in the gff do not match the "chromosome names" in the fasta

Here is a JBrowse FAQ entry regarding this http://gmod.org/wiki/JBrowse_FAQ#After_I_load_my_track_it_appears_in_the_tracklist.2C_but_the_track_appears_empty