This is a quick overview to get started running JBrowse 2 from scratch using the command line. It is helpful if you have some familiarity with the command line, and with some bioinformatics tools like samtools in general to follow these steps. This guide also assumes you have:
- a webserver that reads files from /var/www/html/ e.g. Apache or nginx (not strictly necessary for jbrowse to run, see footnote)
- node 10+ installed
- genometools installed e.g.
sudo apt install genometoolsor
brew install brewsci/bio/genometools, used for sorting GFF3 for creating tabix GFF
- samtools installed e.g.
sudo apt install samtoolsor
brew install samtools, used for creating FASTA index and BAM/CRAM processing
- tabix installed e.g.
sudo apt install tabixor
brew install htslib, used for created tabix indexes for BED/VCF/GFF files
You can now visit http://localhost/jbrowse2 and your genome should be ready!
This guide is meant to be a super-quick conceptual overview for getting jbrowse 2 setup, but if you are new to the command line or to jbrowse in general, you might want to start with the slightly-longer quick-start guide here.
JBrowse doesn't strictly need Apache or nginx, it is "static site compatible" meaning it uses no server side code and can run on any static website hosting. For example, you can upload the jbrowse folder that we prepared here in /var/www/html/jbrowse2 to Amazon S3, and it will work there too. See the FAQ for what webserver do I need for more info.