1. Install build prerequisites, plus make and a C compiler. On Ubuntu, you could do this with below command.
sudo apt-get install zlib1g-dev libpng-dev libgd2-noxpm-dev build-essential
2. Download JBrowse zip file (JBrowse-1.10.12.zip) from http://jbrowse.org/jbrowse-1-11-0/
3. Place the downloaded zip file in /var/www/JBrowse.
4. Unzip the zip file (JBrowse-1.10.12.zip) using the following command.
unzip /var/www/JBrowse/ JBrowse-1.10.12.zip
5. Allow read write access to /var/www/JBrowse folder using the following command.
sudo chown ‘user’ /var/www/JBrowse
6. Make sure you are installed with GD, Libpng & Curl libraries.
7. Run the following command.
sudo apt-get install libpng12-0 libpng12-dev build-essential libcurses5-dev
8. Go inside /var/www/JBrowse/JBrowse-1.10.12/, run ./setup.sh
9. Now you are ready to access JBrowse in your machine. Open internet explorer & type the following url http://localhost/JBrowse/JBrowse-1.10.12/index.htm
What other tools needed for Jbrowse?
Yes the following tools are needed.
bgzip & tabix
- Compress your .vcf file using the bgzip program
- For more information about the bgzip command, run bgzip with no other arguments.
- Create a tabix index file for the bgzip-compressed VCF (.vcf.gz)
tabix -p vcf my.vcf.gz
The tabix command appends .tbi to my.vcf.gz, creating a binary index file my.vcf.gz.tbi with which genomic coordinates can quickly be translated into file offsets in my.vcf.gz.
- Move both the compressed VCF file and tabix index file (my.vcf.gz and my.vcf.gz.tbi) to an http, https, or ftp location.
For more info, please refer – http://genome.ucsc.edu/goldenPath/help/vcf.htm
- Sort and create an index for the BAM
samtools sort my.bam my.sorted
samtools index my.sorted.bam
The sort command appends .bam to my.sorted, creating a BAM file of alignments ordered by leftmost position on the reference assembly. The index command generates a new file, my.sorted.bam.bai, with which genomic coordinates can quickly be translated into file offsets in my.sorted.bam.
- Move both the BAM file and index file (my.sorted.bam and my.sorted.bam.bai) to an http, https, or ftp location.
For more info, please refer – http://genome.ucsc.edu/goldenPath/help/bam.htm