GCATemplates available: no, JBrowse is only available at the HPRC Portal
JBrowse is available on the Terra portal
You will need to index the genome fasta file prior to loading the genome file in JBrowse.
To do this, you will need to go to the Terra Unix command line and index the fasta reference file using samtools which will create a .fai index file
module load SAMtools/1.9-intel-2018b samtools faidx reference_genome.fasta
- Then you start JBrowse in the portal (under the Interactive Apps section) selecting the Number of hours and Number of cores as needed.
- Select 'Open Sequence File' and click the 'Select Files...' button in the 'Local files' section (files that are located on Terra)
- Load the reference_genome.fasta and the reference_genome.fasta.fai at the same time in JBrowse.
- Then you can add tracks (gff, bam, ...) by selecting Track in the JBrowse right panel at the top.
- All files that you add as tracks or genomes must be located on Terra. URLs are not supported since JBrowse on the portal.hprc.tamu.edu runs on the compute nodes which do not have internet access.
- Remember to delete the interactive session when you are finished.