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annotate readme.rst @ 0:d78175596286 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
author fubar
date Mon, 08 Jan 2024 09:20:33 +0000
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d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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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 gunicorn does not support byte range requests, so this tool must be served by nginx
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12 or other web server, correctly configured to support range requests.
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14 Installation
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15 ============
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17 It is recommended to install this wrapper via the Galaxy Tool Shed.
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19 Running Locally
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20 ===============
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22 The Galaxy tool interface writes out a xml file which is then used to generate
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23 the visualizations. An example used during development/testing can be seen in
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24 `test-data/*/test.xml`. The format is in no way rigorously defined and is
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25 likely to change at any time! Beware. ;)
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27 History
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28 =======
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30 - 2.10.0+galaxy2
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32 - UPDATED to JBrowse 2.10.0
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33 - REMOVED most colour and track control from XML and script.
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34 - seems to work well with defaults.
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35 - need to document and implement track settings by running the browser locally.
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36 - works well enough to be useful in workflows such as TreeValGal.
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37 - JB2 seems to set defaults wisely.
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38 - not yet ideal for users who need fine grained track control.
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40 - 1.16.11+galaxy0
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42 - UPDATED to JBrowse 1.16.11
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44 - 1.16.10+galaxy0
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46 - UPDATED to JBrowse 1.16.10
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47 - ADDED GALAXY_JBROWSE_SYMLINKS environment variable: if set, the tool will make symlinks to bam/bigwig files instead of copying them
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49 - 1.16.9+galaxy0
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51 - UPDATED to JBrowse 1.16.9
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53 - 1.16.8+galaxy0
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55 - UPDATED to JBrowse 1.16.8
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57 - 1.16.5+galaxy0
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59 - UPDATED to JBrowse 1.16.5
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61 - 1.16.4+galaxy0
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63 - UPDATED to JBrowse 1.16.4
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64 - ADDED filter too big metadata
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65 - CHANGED default value for topLevelFeatures (gene subfeatures are now inferred) and style.className (feature style was fixed)
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67 - 1.16.2+galaxy0
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69 - UPDATED to JBrowse 1.16.2
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70 - ADDED support for NeatHTMLFeatures and NeatCanvasFeatures track types
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72 - 1.16.1+galaxy0
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74 - UPDATED to JBrowse 1.16.1
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75 - ADDED support for MultiBigWig plugin
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76 - ADDED support for tabix indexing of fasta and gff
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77 - ADDED support for REST and SPARQL endpoints
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78 - ADDED option to change chunk size for BAM tracks
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79 - FIXED loading of VCF files. They were gzipped and the URLs were incorrect
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80 - FIXED metadata on tracks types other than GFF+HTML
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81 - FIXED infrastructure URL parsing (and embedding in links) for some tracks
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82 - REMOVED support for selecting multiple genomes as input due to tracking of track metadata
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83 - REMOVED support for themes as JBrowse no longer allow runtime loading of plugins
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84
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85 - 0.7 Support for plugins (currently GC Content, Bookmarks, ComboTrackSelector),
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86 track metadata
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87 - 0.5.2 Support for CanvasFeatures options.
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88 - 0.5.1 Support for contextual menus. Conda tests.
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89 - 0.5 Update existing instances on disk. Index names. Support HTML tracks
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90 instead of Canvas. Support default tracks. General JBrowse optinos
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91 - 0.4 Support for dataset collections and customisation of tracks including
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92 labelling, colours, styling. Added support for genetic code selection.
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93 Fixed package installation recipe issues.
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94 - 0.3 Added support for BigWig, etc.
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95 - 0.2 Added support for BAM, Blast, VCF.
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96 - 0.1 Initial public release.
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97
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98 Wrapper License (MIT/BSD Style)
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99 ===============================
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100
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101 Permission to use, copy, modify, and distribute this software and its
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102 documentation with or without modifications and for any purpose and
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103 without fee is hereby granted, provided that any copyright notices
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104 appear in all copies and that both those copyright notices and this
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105 permission notice appear in supporting documentation, and that the names
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106 of the contributors or copyright holders not be used in advertising or
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107 publicity pertaining to distribution of the software without specific
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108 prior permission.
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109
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110 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
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111 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
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112 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
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113 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT OR
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114 CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF
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115 USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR
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116 OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR
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117 PERFORMANCE OF THIS SOFTWARE.