annotate readme.rst @ 15:cce8dacb240f draft

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date Thu, 25 Jan 2024 07:39:41 +0000
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1 JBrowse2 in Galaxy
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2 ==================
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4 JBrowse2 is a fast, embeddable genome browser built completely with
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5 JavaScript and HTML5
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7 Thus, it makes an ideal fit with Galaxy, especially for use as a
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8 workflow summary. E.g. annotate a genome, then visualise all of the
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9 associated datasets as an interactive HTML page. This tool MUST be whitelisted
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10 (or ``sanitize_all_html=False`` in galaxy.ini) to function correctly.
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11 The built-in Galaxy gunicorn server does not support byte range requests, so this tool must be proxied by nginx
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12 or another web server, correctly configured to support range requests. A tiny web server is bundled
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13 with each JBrowse2 archive - see below.
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15 Installation
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16 ============
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18 This wrapper is normally installed by a server administrator from the Galaxy Tool Shed IUC JBrowse2 repository.
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20 Local display
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21 =============
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23 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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24 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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25 giving the same view as seen when viewed from the Galaxy history.
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27 From the newly unzipped directory where that file can be found, and with Python3 installed and working,
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29 `python3 jb2_webserver.py`
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31 will open the preconfigured browser using the default web browser application.
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33 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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34
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35 History
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36 =======
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38 - 2.10.0+galaxy2
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39
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40 - UPDATED existing JBrowse1.16.11 code to JBrowse 2.10.0
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41 - was working well enough for VGP when previous PR discovered
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42 - too late to backport all the fixes
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43 - working default session and some other ideas copied instead.
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44 - seems to work well with defaults.
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45 - need to document and implement track settings by running the browser locally.
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46 - works well enough to be useful in workflows such as TreeValGal.
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47 - JB2 seems to set defaults wisely.
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48 - not yet ideal for users who need fine grained track control.
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49 - synteny works.
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52 Wrapper License (MIT/BSD Style)
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53 ===============================
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55 Permission to use, copy, modify, and distribute this software and its
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56 documentation with or without modifications and for any purpose and
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57 without fee is hereby granted, provided that any copyright notices
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58 appear in all copies and that both those copyright notices and this
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59 permission notice appear in supporting documentation, and that the names
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60 of the contributors or copyright holders not be used in advertising or
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61 publicity pertaining to distribution of the software without specific
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62 prior permission.
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63
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64 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
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65 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
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66 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
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67 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT OR
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68 CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF
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69 USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR
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70 OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR
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71 PERFORMANCE OF THIS SOFTWARE.