Mercurial > repos > fubar > jbrowse2

annotate readme.rst @ 90:51980e0dafd2 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11-dirty
author fubar
date Wed, 17 Apr 2024 22:31:52 +0000
parents e7a6f7a7148d
children 74074746ccd8
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1 JBrowse2 in Galaxy
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2 ==================
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3 Added Mar 26:
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4 Testing history added with tests of the 8 simple formats
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5 hic and paf need small tests but work with big ones...
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8 Added Mar 8:
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9 - URI as data source for tracks
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10 - Autogenerate from a collection now builtin to advanced options - ignores form
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11 - potentially thousands of tracks without filling in any form...
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12 - Cram now working
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13 - Multigenome pafs from mashmap working properly..
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14 - TODO reuse code for references for paf references to allow URI and builtin genomes
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16 Added Mar 3:
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17 - optional tracks at last for JB2
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18 - dotted noodles from optional inputs now ignored without harm
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19 - autogenJB2.
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20 - Takes a collection of bam/vcf etc and turns them into tracks in a normal JB2 history item.
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21 - Uses the JbrowseConnector, but the XML tool drives it from the contents of the collection.
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22 - Collection can be built from any source or with optional noodles in a WF
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23 - Produces a JB2 with all available tracks.
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24 - Argparse command line with repeats for tracks and references
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25 - so works outside Galaxy to process directories or s3 buckets.
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28 Added Feb 3: cool/mcool -> hic
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30 .. image:: dm4_in_jb2.png
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32 Other tracks
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34 .. image:: jbrowse8.png
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36 JBrowse2 is a fast, embeddable genome browser built completely with
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37 JavaScript and HTML5
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39 Makes an ideal fit with Galaxy, especially for use as a
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40 workflow summary. E.g. annotate a genome, then visualise all of the
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41 associated datasets as an interactive HTML page. This tool MUST be whitelisted
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42 (or ``sanitize_all_html=False`` in galaxy.ini) to function correctly.
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43 The built-in Galaxy gunicorn server does not support byte range requests, so this tool must be proxied by nginx
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44 or another web server, correctly configured to support range requests. A tiny web server is bundled
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45 with each JBrowse2 archive - see below.
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47 Installation
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48 ============
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49
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50 This wrapper is normally installed by a server administrator from the Galaxy Tool Shed IUC JBrowse2 repository.
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52 Local display
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53 =============
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55 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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56 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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57 giving the same view as seen when viewed from the Galaxy history.
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59 From the newly unzipped directory where that file can be found, and with Python3 installed and working,
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61 `python3 jb2_webserver.py`
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63 will open the preconfigured browser using the default web browser application.
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64
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65 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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66
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67 History
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68 =======
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70 - 2.10.0+galaxy2
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71
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72 - UPDATED existing JBrowse1.16.11 code to JBrowse 2.10.0
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73 - was working well enough for VGP when previous PR discovered
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74 - too late to backport all the fixes
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75 - working default session and some other ideas copied instead.
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76 - seems to work well with defaults.
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77 - need to document and implement track settings by running the browser locally.
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78 - works well enough to be useful in workflows such as TreeValGal.
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79 - JB2 seems to set defaults wisely.
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80 - not yet ideal for users who need fine grained track control.
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81 - synteny (paf + reference) now working
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82 - rehomed at https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 while IUC reviews are slowly sorted out.
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85 Wrapper License (MIT/BSD Style)
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86 ===============================
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87
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88 Permission to use, copy, modify, and distribute this software and its
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89 documentation with or without modifications and for any purpose and
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90 without fee is hereby granted, provided that any copyright notices
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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91 appear in all copies and that both those copyright notices and this
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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92 permission notice appear in supporting documentation, and that the names
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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93 of the contributors or copyright holders not be used in advertising or
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94 publicity pertaining to distribution of the software without specific
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95 prior permission.
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96
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97 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
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98 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
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99 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
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100 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT OR
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101 CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF
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102 USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR
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103 OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR
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104 PERFORMANCE OF THIS SOFTWARE.