This page should be enough to get you started. If you run into trouble, please join the mailing list and ask us about it.
From CPAN:
Get JBrowse from GitHub (click on the "download" button)
Then unzip/untar JBrowse in a directory that's served by apache (e.g., /var/www/html/)
Tell JBrowse about your reference sequences with bin/prepare-refseqs.pl
(JBrowse generates files with links that are relative to the directory where index.html is located, so you should run the JBrowse scripts from that directory)
$ bin/prepare-refseqs.pl --fasta docs/tutorial/data_files/volvox.fa
There are two options for telling JBrowse about your feature data: if you have a genomic annotation database such as chado, Bio::DB::SeqFeature::Store, or Bio::DB::GFF, then you can use JBrowse's biodb-to-json.pl. On the other hand, if you mainly deal with flat files like GFF or BED, it may be more convenient to use JBrowse's flatfile-to-json.pl.
You use bin/biodb-to-json.pl with a configuration file (documented here).
$ bin/biodb-to-json.pl --conf docs/tutorial/conf_files/volvox.json
bin/flatfile-to-json.pl doesn't use a configuration file; instead, per-track settings are given as command-line arguments. Run bin/flatfile-to-json.pl without any arguments to see a description of the available settings. Most of them correspond to track settings in the config file, so see the track settings section in the config file documentation for more details.
If you have data in the BAM format, you can import it into a JBrowse instance using the flatfile-to-json.pl program. Here is one example of a command that does that, using the included data:
bin/flatfile-to-json.pl --bam docs/tutorial/data_files/volvox-sorted.bam --tracklabel bam_simulated --key "Simulated next-gen reads" --cssClass basic --clientConfig '{"featureCss": "background-color: #66F; height: 8px", "histCss": "background-color: #88F"}'
To enable users to search using feature names or IDs, you have to do two things:
$ bin/generate-names.pl -v
You need to run bin/generate-names.pl again every time you add new features to JBrowse.
visit the main page to view the results.
If you want to browse quantitative ("wiggle") tracks in JBrowse, you need to do a bit more work.
Prerequisites:
Compile the wiggle-processing program by running configure and then make in the JBrowse root directory
$ ./configure $ make
You need libpng and a C++ compiler; you can get these from MacPorts or Fink.
Once you have those installed, you need to compile the JBrowse wiggle-processing program. JBrowse includes a makefile to do this, but you may need to add the paths for libpng and png.h to your compiler's library and include paths. For example, if libpng is in /usr/X11, you can run configure like this:
$ ./configure CXXFLAGS=-I/usr/X11/include LDFLAGS=-L/usr/X11/lib
Depending on which OS X you have (and whether you're using MacPorts/fink/etc.), libpng might be somewhere other than /usr/X11, like /opt/local for example. To find where libpng is, try locate libpng
Once wig2png is compiled, you run it via a wrapper script:
$ bin/wig-to-json.pl --wig docs/tutorial/data_files/volvox_microarray.wig