Prereq: You need PuTTY to SSH in, and probably WinSCP too so you can upload the FASTA and GB files.

0) You might have a /html/jbrowse/data/ folder. If so delete it (you will lose whatever you had there!) with rm -rf data

1) Req'd files: Download appropriate FASTA and GB files from the PubMed page for your genome. Upload them into your /html/jbrowse directory. cd into this directory.

2) Create GFF3 file: perl /usr/bin/bp_genbank2gff3.pl MYVIRUS.gb
It will make a MYVIRUS.gb.gff file in the current directory.

3) Split the sequence: bin/prepare-refseqs.pl --fasta MYVIRUS.fasta

3) JSON generation: perl bin/flatfile-to-json-new.pl --gff MYVIRUS.gb.gff --tracklabel Genes --key Genes --getLabel Name

4) Name indexing: bin/generate-names.pl

Go ahead and go to http://www.omgbrowse.com/fall09/omg-##/jbrowse/ .
Your stuff should appear!

NOTE #1: In step 3, that thing after "JSON generation:" is one whole line. NOTE #2: You may have to open your FASTA file, and change the first line to whatever the GenBank file has.

For example, my first line had >gi|38018022|ref|NC_005147.1| Human coronavirus OC43, complete genome However, each feature within the GenBank file was prefaced by NC_005147.

Changing the FASTA file's first line to >NC_005147 should be good, if you encountered problems otherwise.

-- MadhviVenkatesh - 07 Dec 2009