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Repository jbrowse

Name: jbrowse

Owner: iuc

Synopsis: JBrowse Genome Browser integrated as a Galaxy Tool

Detailed description:

JBrowse is a fast, extensible JS+HTML5 genome browser.

This repository contains a couple of tools aimed at building up a complete
JBrowse Genome Browser deployment from raw data files such as gff3, bed, bam,
vcf, blastxml, and more...

The tools produce a ready-to-deploy HTML file and associated processed
datasets, allowing visualization of the genome either from within Galaxy, or
outside of Galaxy.

The tool must be whitelisted for HTML content. If BAM files are displayed, it
must be served from an apache or nginx server implementing sendfile.

https://jbrowse.org

Content homepage: https://jbrowse.org

Development repository: https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse

Link to this repository revision: https://toolshed.g2.bx.psu.edu/view/iuc/jbrowse/2c9e5136b416

Clone this repository: hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/jbrowse

Type: unrestricted

Revision: 0:2c9e5136b416

This revision can be installed: True

Times cloned / installed: 5159

Repository README files - may contain important installation or license information

Readme files

JBrowse in Galaxy ================= JBrowse is a fast, embeddable genome browser built completely with JavaScript and HTML5 Thus, it makes an ideal fit with Galaxy, especially for use as a workflow summary. E.g. annotate a genome, then visualise all of the associated datasets as an interactive HTML page. Installation ============ It is recommended to install this wrapper via the Galaxy Tool Shed History ======= - 0.1 Initial public release Wrapper License (MIT/BSD Style) =============================== Permission to use, copy, modify, and distribute this software and its documentation with or without modifications and for any purpose and without fee is hereby granted, provided that any copyright notices appear in all copies and that both those copyright notices and this permission notice appear in supporting documentation, and that the names of the contributors or copyright holders not be used in advertising or publicity pertaining to distribution of the software without specific prior permission. THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.