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annotate readme.rst @ 41:8774b28235bb draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 8556ea066463f5e112b6ded2c1527011ab1e3b38"
author iuc
date Thu, 31 Dec 2020 16:00:42 +0000
parents 667e17248bfe
children 4542035c1075
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1 JBrowse in Galaxy
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2 =================
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4 JBrowse 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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12 Installation
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13 ============
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15 It is recommended to install this wrapper via the Galaxy Tool Shed.
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17 Running Locally
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18 ===============
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20 The Galaxy tool interface writes out a xml file which is then used to generate
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21 the visualizations. An example used during development/testing can be seen in
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22 `test-data/*/test.xml`. The format is in no way rigorously defined and is
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23 likely to change at any time! Beware. ;)
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25 History
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26 =======
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28 - 1.16.10+galaxy0
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30 - UPDATED to JBrowse 1.16.10
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31 - ADDED GALAXY_JBROWSE_SYMLINKS environment variable: if set, the tool will make symlinks to bam/bigwig files instead of copying them
8774b28235bb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 8556ea066463f5e112b6ded2c1527011ab1e3b38"
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33 - 1.16.9+galaxy0
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35 - UPDATED to JBrowse 1.16.9
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37 - 1.16.8+galaxy0
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39 - UPDATED to JBrowse 1.16.8
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41 - 1.16.5+galaxy0
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43 - UPDATED to JBrowse 1.16.5
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45 - 1.16.4+galaxy0
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47 - UPDATED to JBrowse 1.16.4
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48 - ADDED filter too big metadata
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49 - CHANGED default value for topLevelFeatures (gene subfeatures are now inferred) and style.className (feature style was fixed)
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51 - 1.16.2+galaxy0
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53 - UPDATED to JBrowse 1.16.2
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54 - ADDED support for NeatHTMLFeatures and NeatCanvasFeatures track types
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56 - 1.16.1+galaxy0
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58 - UPDATED to JBrowse 1.16.1
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59 - ADDED support for MultiBigWig plugin
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60 - ADDED support for tabix indexing of fasta and gff
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61 - ADDED support for REST and SPARQL endpoints
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62 - ADDED option to change chunk size for BAM tracks
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63 - FIXED loading of VCF files. They were gzipped and the URLs were incorrect
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64 - FIXED metadata on tracks types other than GFF+HTML
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65 - FIXED infrastructure URL parsing (and embedding in links) for some tracks
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66 - REMOVED support for selecting multiple genomes as input due to tracking of track metadata
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67 - REMOVED support for themes as JBrowse no longer allow runtime loading of plugins
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69 - 0.7 Support for plugins (currently GC Content, Bookmarks, ComboTrackSelector),
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70 track metadata
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71 - 0.5.2 Support for CanvasFeatures options.
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72 - 0.5.1 Support for contextual menus. Conda tests.
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73 - 0.5 Update existing instances on disk. Index names. Support HTML tracks
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74 instead of Canvas. Support default tracks. General JBrowse optinos
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75 - 0.4 Support for dataset collections and customisation of tracks including
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76 labelling, colours, styling. Added support for genetic code selection.
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77 Fixed package installation recipe issues.
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78 - 0.3 Added support for BigWig, etc.
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79 - 0.2 Added support for BAM, Blast, VCF.
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80 - 0.1 Initial public release.
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82 Wrapper License (MIT/BSD Style)
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83 ===============================
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85 Permission to use, copy, modify, and distribute this software and its
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86 documentation with or without modifications and for any purpose and
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87 without fee is hereby granted, provided that any copyright notices
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88 appear in all copies and that both those copyright notices and this
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89 permission notice appear in supporting documentation, and that the names
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90 of the contributors or copyright holders not be used in advertising or
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91 publicity pertaining to distribution of the software without specific
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92 prior permission.
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93
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94 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
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95 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
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96 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
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97 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT OR
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98 CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF
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99 USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR
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100 OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR
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101 PERFORMANCE OF THIS SOFTWARE.