Mercurial > repos > fubar > jbrowse2

annotate readme.rst @ 110:c017111e976a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 9de1453a009c254ab11b16ae8a56cb5c22b131bf-dirty
author fubar
date Sat, 29 Jun 2024 09:10:04 +0000
parents b1260bca5fdc
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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 Added April 2024:
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8 Multiple independent assembly/track sets in the same browser now working
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9 Tests are now far more convincing using the zip outputs to check for files
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10 Automated collection generation is really cool - TODO: need visibility for each track
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11 maf and blastxml are working for test files at least - not yet properly tested.
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12 cool/mcool are converted to hic
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13 vcf, cram, bam, bed, gff, bigwig, hic, cool, blastxml, maf, paf tracks.
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16 Added Mar 26:
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17 Testing history added with tests of the 8 simple formats
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18 hic and paf need small tests but work with big ones...
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20 Added Mar 8:
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21 - URI as data source for tracks
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22 - Autogenerate from a collection now builtin to advanced options - ignores form
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23 - potentially thousands of tracks without filling in any form...
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24 - Cram now working
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25 - Multigenome pafs from mashmap working properly..
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26 - TODO reuse code for references for paf references to allow URI and builtin genomes
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28 Added Mar 3:
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29 - optional tracks at last for JB2
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30 - dotted noodles from optional inputs now ignored without harm
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31 - autogenJB2.
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32 - Takes a collection of bam/vcf etc and turns them into tracks in a normal JB2 history item.
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33 - Uses the JbrowseConnector, but the XML tool drives it from the contents of the collection.
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34 - Collection can be built from any source or with optional noodles in a WF
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35 - Produces a JB2 with all available tracks.
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36 - Argparse command line with repeats for tracks and references
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37 - so works outside Galaxy to process directories or s3 buckets.
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40 Added Feb 3: cool/mcool -> hic
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42 .. image:: dm4_in_jb2.png
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43
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44 Other tracks
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46 .. image:: jb2_samplerMay5.png
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48 JBrowse2 is a fast, embeddable genome browser built completely with
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49 JavaScript and HTML5
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51 Makes an ideal fit with Galaxy, especially for use as a
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52 workflow summary. E.g. annotate a genome, then visualise all of the
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53 associated datasets as an interactive HTML page. This tool MUST be whitelisted
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54 (or ``sanitize_all_html=False`` in galaxy.ini) to function correctly.
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55 The built-in Galaxy gunicorn server does not support byte range requests, so this tool must be proxied by nginx
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56 or another web server, correctly configured to support range requests. A tiny web server is bundled
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57 with each JBrowse2 archive - see below.
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59 Installation
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60 ============
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61
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62 This wrapper is normally installed by a server administrator from the Galaxy Tool Shed IUC JBrowse2 repository.
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64 Local display
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65 =============
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66
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67 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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68 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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69 giving the same view as seen when viewed from the Galaxy history.
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71 From the newly unzipped directory where that file can be found, and with Python3 installed and working,
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73 `python3 jb2_webserver.py`
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75 will open the preconfigured browser using the default web browser application.
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76
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77 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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78
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79 History
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80 =======
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82 - 2.10.0+galaxy2
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83
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84 - UPDATED existing JBrowse1.16.11 code to JBrowse 2.10.0
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85 - was working well enough for VGP when previous PR discovered
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86 - too late to backport all the fixes
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87 - working default session and some other ideas copied instead.
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88 - seems to work well with defaults.
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89 - need to document and implement track settings by running the browser locally.
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90 - works well enough to be useful in workflows such as TreeValGal.
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91 - JB2 seems to set defaults wisely.
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92 - not yet ideal for users who need fine grained track control.
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93 - synteny (paf + reference) now working
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94 - rehomed at https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 while IUC reviews are slowly sorted out.
0
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95
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96
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97 Wrapper License (MIT/BSD Style)
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98 ===============================
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99
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100 Permission to use, copy, modify, and distribute this software and its
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101 documentation with or without modifications and for any purpose and
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102 without fee is hereby granted, provided that any copyright notices
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103 appear in all copies and that both those copyright notices and this
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104 permission notice appear in supporting documentation, and that the names
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105 of the contributors or copyright holders not be used in advertising or
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106 publicity pertaining to distribution of the software without specific
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107 prior permission.
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108
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109 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
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110 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
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111 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
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112 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT OR
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113 CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF
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114 USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR
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115 OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR
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116 PERFORMANCE OF THIS SOFTWARE.