cassava_example set up

ssh [email protected]
cd /export/prod/jbrowse_cassavabase/current/data
sudo mkdir cassava_example
cd cassava_example/
sudo mkdir data_files
cd data_files/
sudo ln -s /export/prod/public_cassava/Manihot_v6.1/ .
cd ../
sudo ../../bin/prepare-refseqs.pl --fasta data_files/Manihot_v6.1/assembly/Mesculenta_305_v6.fa
sudo mv data/* .
sudo rm -r data

sudo ../../bin/prepare-refseqs.pl --fasta data_files/Manihot_v6.1/annotation/Mesculenta_305_v6.1.cds.fa.gz --trackLabel CDS --key CDS with# alternative splice variants --seqtype dna

sudo ../../bin/flatfile-to-json.pl --gff data_files/Manihot_v6.1/annotation/Mesculenta_305_v6.1.gene.gff3 --trackType CanvasFeatures -trackLabel genes --clientConfig '{"description" : "note,description", "label" : "note,name,id" }' --metadata '{"category" : "mRNA"}' --out ./

sudo ../../bin/flatfile-to-json.pl --gff data_files/Manihot_v6.1/annotation/Mesculenta_305_v6.1.gene_exons.gff3 --trackType CanvasFeatures -trackLabel exons --clientConfig '{"description" : "note,description", "label" : "note,name,id" }' --metadata '{"category" : "mRNA"}' --out ./

cd ../../
sudo emacs jbrowse.conf
add the following to the end of the file:

[datasets.cassava_example]
url  = ?data=data/cassava_example
name = cassava_example