How to set up JBrowse Web on a school server (group Linux machine)

This tutorial teaches how to set up JBrowse2 Web application on an intranet server. You need administrator rights for this.

1. Install Node.js LTS on Ubuntu

• Installation instructions

# Install the LTS version 
curl -fsSL https://deb.nodesource.com/setup_lts.x | sudo -E bash - &&\
sudo apt-get install -y nodejs

• Test installation using

node -v
npm version 

2. Install Samtools

sudo apt update
sudo apt install samtools
samtools --version

3. Install tabix

sudo apt install tabix
tabix --version

4. Install genometools

sudo apt install genometools
genometools --version 

5. Install JBrowse CLI

sudo npm install -g @jbrowse/cli
jbrowse --version

6. Download and unzip JBrowse2 Web

cd ~
wget https://github.com/GMOD/jbrowse-components/releases/download/v2.5.0/jbrowse-web-v2.5.0.zip
mkdir jbrowse2
unzip jbrowse-web-v2.5.0.zip -d jbrowse2/

7. Install Apache2

sudo apt install apache2

After installation, Apache2 should start automatically. You can verify its status by runnning:

sudo systemctl status apache2

8. Put the Jbrowse2 Web folder into the folder /var/www/html/

sudo cp -r ~/jbrowse2 /var/www/html

9. Get the IP address of your server

First, we need to remove the index.html file in the folder /var/www/html/:

sudo rm /var/www/html/index.html

Then, get the IP address of your server:

hostname -I 

Then, in the browser go to the address http://your_ip_address. You should see a Welcome page.

Finally, you can read this tutorial for adding tracks and etc.

10. Example code for adding a track

Here, we use the Arabidopsis genome as an example.

mkdir ~/genome
cd ~/genome
wget https://www.arabidopsis.org/download_files/Genes/TAIR10_genome_release/TAIR10_chromosome_files/TAIR10_chr_all.fas.gz
gunzip TAIR10_chr_all.fas.gz 
mv TAIR10_chr_all.fas TAIR10_chr_all.fa
samtools faidx TAIR10_chr_all.fa
sudo jbrowse add-assembly TAIR10_chr_all.fa --load copy --out /var/www/html/jbrowse2  

Then, go to the website http://your_ip_address, you should see there are options for creating a new session.

References

• JBrowse web setup using the CLI
• I downloaded jbrowse2 using the command line interface, but encountered an error that prevented the page from loading. #3684
• How to install Node.js via binary archive on Linux
• Jbrowse
• nodejs.org
• ChatGPT