jbrowse-plugin-hgb

JBrowse2 plugin for displaying long-read alignments by hgb.

Screenshots

Prerequisites

• Rust nightly
• Node.js
• Python3 (optional)

Getting Started (Single Track)

The input bam file needs to be attached MD tags by samtools calmd and indexed by samtools index.

• Docker

docker run --rm -ti -p 9000:9000 -v `pwd`:/data 6thbridge/jbrowse2-hgb:master /data/<input.bam>

• Singularity

singularity build jb2-hgb.sif docker://6thbridge/jbrowse2-hgb:master
singularity -s run jb2-hgb.sif <input.bam>

Access to http://localhost:9000/static/index.html.

Getting Started (Multiple Tracks)

JBrowse2-HGB works with Toil on HPC environments where communication between compute nodes is allowed and jobs are needed to be submitted using batch job system.

• Preparation

pip install virtualenv
virtualenv ~/venv
source ~/venv/bin/activate
pip install toil nginx-config-builder portpicker https://github.com/6br/toil_container

npm install -g @jbrowse/cli

• Single Node

python3 hgb.py jobstore --bam <input_bam> --track-names <track_name> --singularity docker://6thbridge/hgb:master

• Multiple Nodes w/ Batch Job Engine

python3 hgb.py jobstore --track-names BAM1 BAM2 BAM3 --bam bam1.bam bam2.bam bam3.bam --auth user:pass --singularity docker://6thbridge/hgb:master --disableCaching --batchSystem grid_engine --deadlockWait 200 --maxServiceJobs 10 --realTimeLogging

# An example for a grid engine:
TOIL_GRIDENGINE_PE='def_slot' TOIL_GRIDENGINE_ARGS="-l s_vmem=15G,mem_req=15G" python3 hgb2.py jobstore --track-names BAM1 BAM2 BAM3 --bam bam1.bam bam2.bam bam3.bam --auth user:pass --singularity docker://6thbridge/hgb:master --manualMemArgs --disableCaching --batchSystem grid_engine --deadlockWait 200 --maxServiceJobs 10 --realTimeLogging

After all servers are prepared, the message is displayed in red letters on the stdout of the leader process of Toil as follows:

2022-01-13 16:12:25 toil-rt [pid 72140]
CRITICAL:Access to http://<hostname>:<port>

Please access to http://<hostname>:<port>.

Manual Deploy

STEP1: Serve HGB server

bash -x start_hgb_server.sh $NUM_OF_THREADS $LOCATION_OF_BAM
bash -x start_hgb_server.sh $NUM_OF_THREADS $LOCATION_OF_BAM 0.0.0.0:5000

STEP2: Start JBrowse2

The following command needs to run on another shell.

bash -x start_jbrowse_hgb.sh 
bash -x start_jbrowse_hgb.sh $HGB_SERVER_URL 38
bash -x start_jbrowse_hgb.sh $HGB_SERVER_URL 19

You can specify reference genome as the second argument as 38 or 19 (hg38 or hg19, respectively).

Usage in jbrowse-web

Add to the "plugins" of your JBrowse Web config. The unpkg CDN should be stable, or you can download the js file to your server.

{
  "plugins": [
    {
      "name": "hgb",
      "url": "https://unpkg.com/jbrowse-plugin-hgb/dist/jbrowse-plugin-hgb.umd.production.min.js"
    }
  ]
}

This plugin is currently quite basic, and there is no mouseover interactivity or drawn labels on features

For use in jbrowse/react-linear-genome-view

See DEVELOPMENT