Mercurial > repos > fubar > jbrowse2

comparison readme.rst @ 97:74074746ccd8 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
author fubar
date Sat, 01 Jun 2024 05:37:13 +0000
parents e7a6f7a7148d
children b1260bca5fdc
comparison
equal deleted inserted replaced
96:5ef1ba2031f2 97:74074746ccd8
1 JBrowse2 in Galaxy 1 JBrowse2 in Galaxy
2 ================== 2 ==================
3
4
5 Added April 2024:
6 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
8 Automated collection generation is really cool - TODO: need visibility for each track
9 maf and blastxml are working for test files at least - not yet properly tested.
10 cool/mcool are converted to hic
11 vcf, cram, bam, bed, gff, bigwig, hic, cool, blastxml, maf, paf tracks.
12
13
3 Added Mar 26: 14 Added Mar 26:
4 Testing history added with tests of the 8 simple formats 15 Testing history added with tests of the 8 simple formats
5 hic and paf need small tests but work with big ones... 16 hic and paf need small tests but work with big ones...
6 17
7 18
27 38
28 Added Feb 3: cool/mcool -> hic 39 Added Feb 3: cool/mcool -> hic
29 40
30 .. image:: dm4_in_jb2.png 41 .. image:: dm4_in_jb2.png
31 42
32 Other tracks 43 Other samples
33 44
34 .. image:: jbrowse8.png 45 .. image:: jb2_samplerMay5.png
35 46
36 JBrowse2 is a fast, embeddable genome browser built completely with 47 JBrowse2 is a fast, embeddable genome browser built completely with
37 JavaScript and HTML5 48 JavaScript and HTML5
38 49
39 Makes an ideal fit with Galaxy, especially for use as a 50 Makes an ideal fit with Galaxy, especially for use as a
67 History 78 History
68 ======= 79 =======
69 80
70 - 2.10.0+galaxy2 81 - 2.10.0+galaxy2
71 82
72 - UPDATED existing JBrowse1.16.11 code to JBrowse 2.10.0 83 - UPDATED existing JBrowse1.16.11 code to JBrowse 2.10.0
73 - was working well enough for VGP when previous PR discovered 84 - was working well enough for VGP when previous PR discovered
74 - too late to backport all the fixes 85 - too late to backport all the fixes
75 - working default session and some other ideas copied instead. 86 - working default session and some other ideas copied instead.
76 - seems to work well with defaults. 87 - seems to work well with defaults.
77 - need to document and implement track settings by running the browser locally. 88 - need to document and implement track settings by running the browser locally.
78 - works well enough to be useful in workflows such as TreeValGal. 89 - works well enough to be useful in workflows such as TreeValGal.
79 - JB2 seems to set defaults wisely. 90 - JB2 seems to set defaults wisely.
80 - not yet ideal for users who need fine grained track control. 91 - not yet ideal for users who need fine grained track control.
81 - synteny (paf + reference) now working 92 - synteny (paf + reference) now working
82 - rehomed at https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 while IUC reviews are slowly sorted out. 93 - rehomed at https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 while IUC reviews are slowly sorted out.
83 94
84 95
85 Wrapper License (MIT/BSD Style) 96 Wrapper License (MIT/BSD Style)
86 =============================== 97 ===============================
87 98