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comparison readme.rst @ 98:b1260bca5fdc draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
author bgruening
date Wed, 05 Jun 2024 10:00:07 +0000
parents 74074746ccd8
children
comparison
equal deleted inserted replaced
97:74074746ccd8 98:b1260bca5fdc
1 JBrowse2 in Galaxy 1 JBrowse2 in Galaxy
2 ================== 2 ==================
3 3
4 JBrowse2 is a fast, embeddable genome browser built completely with
5 JavaScript and HTML5
4 6
5 Added April 2024: 7 Added April 2024:
6 Multiple independent assembly/track sets in the same browser now working 8 Multiple independent assembly/track sets in the same browser now working
7 Tests are now far more convincing using the zip outputs to check for files 9 Tests are now far more convincing using the zip outputs to check for files
8 Automated collection generation is really cool - TODO: need visibility for each track 10 Automated collection generation is really cool - TODO: need visibility for each track
12 14
13 15
14 Added Mar 26: 16 Added Mar 26:
15 Testing history added with tests of the 8 simple formats 17 Testing history added with tests of the 8 simple formats
16 hic and paf need small tests but work with big ones... 18 hic and paf need small tests but work with big ones...
17
18 19
19 Added Mar 8: 20 Added Mar 8:
20 - URI as data source for tracks 21 - URI as data source for tracks
21 - Autogenerate from a collection now builtin to advanced options - ignores form 22 - Autogenerate from a collection now builtin to advanced options - ignores form
22 - potentially thousands of tracks without filling in any form... 23 - potentially thousands of tracks without filling in any form...
38 39
39 Added Feb 3: cool/mcool -> hic 40 Added Feb 3: cool/mcool -> hic
40 41
41 .. image:: dm4_in_jb2.png 42 .. image:: dm4_in_jb2.png
42 43
43 Other samples 44 Other tracks
44 45
45 .. image:: jb2_samplerMay5.png 46 .. image:: jb2_samplerMay5.png
46 47
47 JBrowse2 is a fast, embeddable genome browser built completely with 48 JBrowse2 is a fast, embeddable genome browser built completely with
48 JavaScript and HTML5 49 JavaScript and HTML5
78 History 79 History
79 ======= 80 =======
80 81
81 - 2.10.0+galaxy2 82 - 2.10.0+galaxy2
82 83
83 - UPDATED existing JBrowse1.16.11 code to JBrowse 2.10.0 84 - UPDATED existing JBrowse1.16.11 code to JBrowse 2.10.0
84 - was working well enough for VGP when previous PR discovered 85 - was working well enough for VGP when previous PR discovered
85 - too late to backport all the fixes 86 - too late to backport all the fixes
86 - working default session and some other ideas copied instead. 87 - working default session and some other ideas copied instead.
87 - seems to work well with defaults. 88 - seems to work well with defaults.
88 - need to document and implement track settings by running the browser locally. 89 - need to document and implement track settings by running the browser locally.
89 - works well enough to be useful in workflows such as TreeValGal. 90 - works well enough to be useful in workflows such as TreeValGal.
90 - JB2 seems to set defaults wisely. 91 - JB2 seems to set defaults wisely.
91 - not yet ideal for users who need fine grained track control. 92 - not yet ideal for users who need fine grained track control.
92 - synteny (paf + reference) now working 93 - synteny (paf + reference) now working
93 - rehomed at https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 while IUC reviews are slowly sorted out. 94 - rehomed at https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 while IUC reviews are slowly sorted out.
94 95
95 96
96 Wrapper License (MIT/BSD Style) 97 Wrapper License (MIT/BSD Style)
97 =============================== 98 ===============================
98 99