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comparison readme.rst @ 7:b04fd993b31e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
author fubar
date Wed, 17 Jan 2024 07:50:52 +0000
parents d78175596286
children c60b17456297
comparison
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6:79f7265f90bd 7:b04fd993b31e
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7 Thus, it makes an ideal fit with Galaxy, especially for use as a 7 Thus, it makes an ideal fit with Galaxy, especially for use as a
8 workflow summary. E.g. annotate a genome, then visualise all of the 8 workflow summary. E.g. annotate a genome, then visualise all of the
9 associated datasets as an interactive HTML page. This tool MUST be whitelisted 9 associated datasets as an interactive HTML page. This tool MUST be whitelisted
10 (or ``sanitize_all_html=False`` in galaxy.ini) to function correctly. 10 (or ``sanitize_all_html=False`` in galaxy.ini) to function correctly.
11 gunicorn does not support byte range requests, so this tool must be served by nginx 11 The built-in Galaxy gunicorn server does not support byte range requests, so this tool must be proxied by nginx
12 or other web server, correctly configured to support range requests. 12 or another web server, correctly configured to support range requests. A tiny web server is bundled
13 with each JBrowse2 archive - see below.
13 14
14 Installation 15 Installation
15 ============ 16 ============
16 17
17 It is recommended to install this wrapper via the Galaxy Tool Shed. 18 This wrapper is normally installed by a server administrator from the Galaxy Tool Shed IUC JBrowse2 repository.
18 19
19 Running Locally 20 Local display
20 =============== 21 =============
21 22
22 The Galaxy tool interface writes out a xml file which is then used to generate 23 Each JBrowse2 history item can be downloaded ("floppy disk" icon) to your local disk. There, it can be unzipped into a new directory.
23 the visualizations. An example used during development/testing can be seen in 24 That directory includes a python script, *jb2_webserver.py* that will run a local web server able to serve byte range requests,
24 `test-data/*/test.xml`. The format is in no way rigorously defined and is 25 giving the same view as seen when viewed from the Galaxy history.
25 likely to change at any time! Beware. ;) 26
27 From the newly unzipped directory where that file can be found, and with Python3 installed and working,
28
29 `python3 jb2_webserver.py`
30
31 will open the preconfigured browser using the default web browser application.
26 32
27 History 33 History
28 ======= 34 =======
29 35
30 - 2.10.0+galaxy2 36 - 2.10.0+galaxy2
31 37
32 - UPDATED to JBrowse 2.10.0 38 - UPDATED existing JBrowse1.16.11 code to JBrowse 2.10.0
33 - REMOVED most colour and track control from XML and script.
34 - seems to work well with defaults. 39 - seems to work well with defaults.
35 - need to document and implement track settings by running the browser locally. 40 - need to document and implement track settings by running the browser locally.
36 - works well enough to be useful in workflows such as TreeValGal. 41 - works well enough to be useful in workflows such as TreeValGal.
37 - JB2 seems to set defaults wisely. 42 - JB2 seems to set defaults wisely.
38 - not yet ideal for users who need fine grained track control. 43 - not yet ideal for users who need fine grained track control.
39 44
40 - 1.16.11+galaxy0
41
42 - UPDATED to JBrowse 1.16.11
43
44 - 1.16.10+galaxy0
45
46 - UPDATED to JBrowse 1.16.10
47 - ADDED GALAXY_JBROWSE_SYMLINKS environment variable: if set, the tool will make symlinks to bam/bigwig files instead of copying them
48
49 - 1.16.9+galaxy0
50
51 - UPDATED to JBrowse 1.16.9
52
53 - 1.16.8+galaxy0
54
55 - UPDATED to JBrowse 1.16.8
56
57 - 1.16.5+galaxy0
58
59 - UPDATED to JBrowse 1.16.5
60
61 - 1.16.4+galaxy0
62
63 - UPDATED to JBrowse 1.16.4
64 - ADDED filter too big metadata
65 - CHANGED default value for topLevelFeatures (gene subfeatures are now inferred) and style.className (feature style was fixed)
66
67 - 1.16.2+galaxy0
68
69 - UPDATED to JBrowse 1.16.2
70 - ADDED support for NeatHTMLFeatures and NeatCanvasFeatures track types
71
72 - 1.16.1+galaxy0
73
74 - UPDATED to JBrowse 1.16.1
75 - ADDED support for MultiBigWig plugin
76 - ADDED support for tabix indexing of fasta and gff
77 - ADDED support for REST and SPARQL endpoints
78 - ADDED option to change chunk size for BAM tracks
79 - FIXED loading of VCF files. They were gzipped and the URLs were incorrect
80 - FIXED metadata on tracks types other than GFF+HTML
81 - FIXED infrastructure URL parsing (and embedding in links) for some tracks
82 - REMOVED support for selecting multiple genomes as input due to tracking of track metadata
83 - REMOVED support for themes as JBrowse no longer allow runtime loading of plugins
84
85 - 0.7 Support for plugins (currently GC Content, Bookmarks, ComboTrackSelector),
86 track metadata
87 - 0.5.2 Support for CanvasFeatures options.
88 - 0.5.1 Support for contextual menus. Conda tests.
89 - 0.5 Update existing instances on disk. Index names. Support HTML tracks
90 instead of Canvas. Support default tracks. General JBrowse optinos
91 - 0.4 Support for dataset collections and customisation of tracks including
92 labelling, colours, styling. Added support for genetic code selection.
93 Fixed package installation recipe issues.
94 - 0.3 Added support for BigWig, etc.
95 - 0.2 Added support for BAM, Blast, VCF.
96 - 0.1 Initial public release.
97 45
98 Wrapper License (MIT/BSD Style) 46 Wrapper License (MIT/BSD Style)
99 =============================== 47 ===============================
100 48
101 Permission to use, copy, modify, and distribute this software and its 49 Permission to use, copy, modify, and distribute this software and its