JBrowse2Server

create a run a local instance of jbrowse2

Usage

This program is now part of the main jvarkit tool. See jvarkit for compiling.

Usage: java -jar dist/jvarkit.jar jbrowse2  [options] Files

Usage: jbrowse2 [options] Files
  Options:
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    --port
      server port.
      Default: 8080
  * -R, --reference
      Indexed fasta Reference file. This file must be indexed with samtools 
      faidx and with picard/gatk CreateSequenceDictionary or samtools dict
    --version
      print version and exit
    --zip
      JBrowse2 archive source
      Default: https://github.com/GMOD/jbrowse-components/releases/download/v4.1.14/jbrowse-web-v4.1.14.zip

Keywords

• jbrowse
• browser
• genome

Creation Date

20250404

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/jbrowse2/JBrowse2Server.java

Contribute

• Issue Tracker: http://github.com/lindenb/jvarkit/issues
• Source Code: http://github.com/lindenb/jvarkit

License

The project is licensed under the MIT license.

Citing

Should you cite jbrowse2 ? https://github.com/mr-c/shouldacite/blob/master/should-I-cite-this-software.md

The current reference is:

http://dx.doi.org/10.6084/m9.figshare.1425030

Lindenbaum, Pierre (2015): JVarkit: java-based utilities for Bioinformatics. figshare. http://dx.doi.org/10.6084/m9.figshare.1425030

Example

java -jar dist/jeter12.jar -R src/test/resources/rotavirus_rf.fa src/test/resources/S*.bam