2023 Class
Many different browser environments
See https://jbrowse.org/jb2/docs/combined/
(some of this was first written by: Tania Kurbessoian @tania-k )
To visualize genome annotation combined with Epigenomic, Transcriptomic, or Variant data you you want to visualize them onto a genome browser. JBrowse provides an easy to setup tool for this visuzalition.
There is substantial documentation that describes installation and add-on features. The FAQ is also incredibly helpful.
These steps will show you how to setup JBrowse on HPCC with some already installed systems to make it easier for you
First you need to configure your account to be able to share data via the web.
Follow the directions on the HPCC manual so that you can configure your home folder ~/.html to be able to serve up data. If you do not want to make everything in this folder public you can use some simple strategies to enable a password protected space by creating a .htaccess file or you can use a web form of security - security through obscurity.
mkdir ~/.html/private
chmod 711 ~/.html/private
mkdir ~/.html/private/MYSECRETPROJECT
# install jbrowse or data or others in ~/.html/private/MYSEKR1TPROJECT
On the web a user browsing will not have permission to see https://cluster.hpcc.ucr.edu/~YOURUSERNAME/private but the URL https://cluster.hpcc.ucr.edu/~YOURUSERNAME/private/MYSEKR1TPROJECT will be visible. This is called security by obscurity, if you generate a long random string instead of MYSEKR1TPROJECT it would be hard to guess it (though note this not really secure since anyone reading network traffic and see the string would now know the the URL to go to).
Generally if you want to protect the data, setup a .htaccess/.htpasswd to require logging in. Making an htpasswd file
The next directions are specific to the UCR HPCC. These instructions use an already build conda environment which you can link to:
# startup an interactive job on the cluster
srun -p short -N 1 -n 4 --mem 16gb --pty bash -l
mkdir -p ~/bigdata/jbrowse2
cd ~/.html/private
ln -s ~/bigdata/jbrowse2 .
cd ~/.html/private/jbrowse2
module load jbrowse2
jbrowse create SARS-CoV-2
If you are going to support multiple JBrowse environments you only need to have a custom data folder. So you can symlink to all the files within the jbrowse checkout and then make a separate data folder too. Otherwise you need to make sure you have a separate custom jbrowse checkout for each project you are supporting.
To download the SARS genome and annotation from NCBI - this can be either in the folder you want to put the data or you can later symlink or copy from this folder
curl -o NC_045512.fna.gz https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/858/895/GCF_009858895.2_ASM985889v3/GCF_009858895.2_ASM985889v3_genomic.fna.gz
curl -o NC_045512.gff.gz https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/858/895/GCF_009858895.2_ASM985889v3/GCF_009858895.2_ASM985889v3_genomic.gff.gz
gunzip NC_045512.fna.gz
module load samtools
samtools faidx NC_045512.fna
# to load GFF we need to ensure it is sorted
module load bcftools
zgrep "^#" NC_045512.gff.gz > header
zgrep -v "^#" NC_045512.gff.gz | sort -k1,1 -k4,4n > NC_045512.sorted.gff
bgzip -i NC_045512.sorted.gff
tabix NC_045512.sorted.gff.gz
To load genome you have already put in the SARS-CoV-2 folder - you need to GO INTO THE SARS-CoV-2 folder
cd SARS-CoV-2
# if downloaded the data into the folder
jbrowse add-assembly NC_045512.fna --load inPlace
# if you had a different folder for this
jbrowse add-assembly ../path/to/NC_045512.fna --load symlink
# if you forgot to create the index it will give you a message
# then you need to do
# samtools faidx NC_045512.fna
# if you created the gff and ran bgzip and tabix in this folder
jbrowse add-track NC_045512.sorted.gff.gz --load inPlace
# if you had put this in another folder
#jbrowse add-track ../path/to/NC_045512.sorted.gff.gz --load symlink
To load VCF files (SNPs and variants)
jbrowse add-track ../path/to/SARS-CoV-2.vcf.gz --load symlink
# if there are warnings you need to build an index you can srun
# module load bcftools
# tabix ../path/to/SARS-CoV-2.vcf.gz
# then re-run the add-track
# if VCF file is in this directory
# jbrowse add-track SARS-CoV-2.vcf.gz --load inPlace
To load BAM files, WIG files, or other gFF you can use same add-track. For BAM, CRAM, files they need to have been indexed
module load samtools
samtools index SRR11140748.bam
To add this file you can do
jbrowse add-track ../path/to/SRR11140748.bam --load symlink
# or if the file was made IN this directory
jbrowse add-track SRR11140748.bam --load inPlace
# if it gives you a warning about index file run
# samtools index BAMFILE
Note that on the UCR HPCC to serve up BAM files properly you need to create a .htaccess file in the jbrowse folder (remember ours is called SARS-CoV-2 in this example).
Contents should be
# This Apache .htaccess file is for
# allowing cross-origin requests as defined by the Cross-Origin
# Resource Sharing working draft from the W3C
# (http://www.w3.org/TR/cors/). In order for Apache to pay attention
# to this, it must have mod_headers enabled, and its AllowOverride
# configuration directive must allow FileInfo overrides.
<IfModule mod_headers.c>
AddType application/octet-stream .bam .bami .bai
Header onsuccess set Access-Control-Allow-Origin *
Header onsuccess set Access-Control-Allow-Headers X-Requested-With,Range
Header onsuccess set Access-Control-Expose-Headers Content-Length,Content-Range
</IfModule>
Now navigate to the web with you link based on your username and folder - this would look like this but you need to put your username http://cluster.hpcc.ucr.edu/~USERNAME/private/jbrowse2/SARS-CoV-2
To see my example go to http://cluster.hpcc.ucr.edu/~jstajich/private/jbrowse2/SARS-CoV-2/