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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit d733fb18a02929c9e9959ad30bd0f1368118e924-dirty
author fubar
date Wed, 07 Feb 2024 22:37:10 +0000
parents fb6cc7bc24df
children 4181e97c70a7
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1 JBrowse2 in Galaxy
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2 ==================
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4 Added Feb 3: cool/mcool -> hic
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6 .. image:: dm4_in_jb2.png
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8 Other tracks
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10 .. image:: jbrowse8.png
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12 JBrowse2 is a fast, embeddable genome browser built completely with
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13 JavaScript and HTML5
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15 Thus, it makes an ideal fit with Galaxy, especially for use as a
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16 workflow summary. E.g. annotate a genome, then visualise all of the
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17 associated datasets as an interactive HTML page. This tool MUST be whitelisted
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18 (or ``sanitize_all_html=False`` in galaxy.ini) to function correctly.
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19 The built-in Galaxy gunicorn server does not support byte range requests, so this tool must be proxied by nginx
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20 or another web server, correctly configured to support range requests. A tiny web server is bundled
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21 with each JBrowse2 archive - see below.
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23 Installation
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24 ============
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26 This wrapper is normally installed by a server administrator from the Galaxy Tool Shed IUC JBrowse2 repository.
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28 Local display
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29 =============
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31 Each JBrowse2 history item can be downloaded ("floppy disk" icon) to your local disk. There, it can be unzipped into a new directory.
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32 That directory includes a python script, *jb2_webserver.py* that will run a local web server able to serve byte range requests,
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33 giving the same view as seen when viewed from the Galaxy history.
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35 From the newly unzipped directory where that file can be found, and with Python3 installed and working,
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37 `python3 jb2_webserver.py`
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39 will open the preconfigured browser using the default web browser application.
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41 That webserver code is separately under the Apache 2 license copied in this repository. See below for this code's MIT license.
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43 History
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44 =======
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46 - 2.10.0+galaxy2
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48 - UPDATED existing JBrowse1.16.11 code to JBrowse 2.10.0
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49 - was working well enough for VGP when previous PR discovered
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50 - too late to backport all the fixes
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51 - working default session and some other ideas copied instead.
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52 - seems to work well with defaults.
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53 - need to document and implement track settings by running the browser locally.
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54 - works well enough to be useful in workflows such as TreeValGal.
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55 - JB2 seems to set defaults wisely.
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56 - not yet ideal for users who need fine grained track control.
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57 - synteny (paf + reference) now working
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58 - rehomed at https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 while IUC reviews are slowly sorted out.
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61 Wrapper License (MIT/BSD Style)
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62 ===============================
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64 Permission to use, copy, modify, and distribute this software and its
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65 documentation with or without modifications and for any purpose and
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66 without fee is hereby granted, provided that any copyright notices
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67 appear in all copies and that both those copyright notices and this
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68 permission notice appear in supporting documentation, and that the names
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69 of the contributors or copyright holders not be used in advertising or
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70 publicity pertaining to distribution of the software without specific
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71 prior permission.
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72
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73 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
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74 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
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75 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
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76 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT OR
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77 CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF
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78 USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR
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79 OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR
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80 PERFORMANCE OF THIS SOFTWARE.