Mercurial > repos > fubar > jbrowse2
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 1a20cf06627d429a211427753f223467188dbe7f-dirty
author | fubar |
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date | Thu, 25 Jan 2024 07:58:28 +0000 |
parents | cce8dacb240f |
children | 4c201a3d4755 |
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JBrowse2 in Galaxy ================== JBrowse2 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. This tool MUST be whitelisted (or ``sanitize_all_html=False`` in galaxy.ini) to function correctly. The built-in Galaxy gunicorn server does not support byte range requests, so this tool must be proxied by nginx or another web server, correctly configured to support range requests. A tiny web server is bundled with each JBrowse2 archive - see below. Installation ============ This wrapper is normally installed by a server administrator from the Galaxy Tool Shed IUC JBrowse2 repository. Local display ============= Each JBrowse2 history item can be downloaded ("floppy disk" icon) to your local disk. There, it can be unzipped into a new directory. That directory includes a python script, *jb2_webserver.py* that will run a local web server able to serve byte range requests, giving the same view as seen when viewed from the Galaxy history. From the newly unzipped directory where that file can be found, and with Python3 installed and working, `python3 jb2_webserver.py` will open the preconfigured browser using the default web browser application. That webserver code is separately under the Apache 2 license copied in this repository. See below for this code's MIT license. History ======= - 2.10.0+galaxy2 - UPDATED existing JBrowse1.16.11 code to JBrowse 2.10.0 - was working well enough for VGP when previous PR discovered - too late to backport all the fixes - working default session and some other ideas copied instead. - seems to work well with defaults. - need to document and implement track settings by running the browser locally. - works well enough to be useful in workflows such as TreeValGal. - JB2 seems to set defaults wisely. - not yet ideal for users who need fine grained track control. - synteny works. 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.