Mercurial > repos > fubar > jbrowse2
diff readme.rst @ 97:74074746ccd8 draft
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 |
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--- a/readme.rst Thu Apr 25 07:25:52 2024 +0000 +++ b/readme.rst Sat Jun 01 05:37:13 2024 +0000 @@ -1,5 +1,16 @@ JBrowse2 in Galaxy ================== + + +Added April 2024: +Multiple independent assembly/track sets in the same browser now working +Tests are now far more convincing using the zip outputs to check for files +Automated collection generation is really cool - TODO: need visibility for each track +maf and blastxml are working for test files at least - not yet properly tested. +cool/mcool are converted to hic +vcf, cram, bam, bed, gff, bigwig, hic, cool, blastxml, maf, paf tracks. + + Added Mar 26: Testing history added with tests of the 8 simple formats hic and paf need small tests but work with big ones... @@ -29,9 +40,9 @@ .. image:: dm4_in_jb2.png -Other tracks +Other samples -.. image:: jbrowse8.png +.. image:: jb2_samplerMay5.png JBrowse2 is a fast, embeddable genome browser built completely with JavaScript and HTML5 @@ -69,17 +80,17 @@ - 2.10.0+galaxy2 - - UPDATED existing JBrowse1.16.11 code to JBrowse 2.10.0 - - was working well enough for VGP when previous PR discovered - - too late to backport all the fixes - - working default session and some other ideas copied instead. - - seems to work well with defaults. - - need to document and implement track settings by running the browser locally. - - works well enough to be useful in workflows such as TreeValGal. - - JB2 seems to set defaults wisely. - - not yet ideal for users who need fine grained track control. - - synteny (paf + reference) now working - - rehomed at https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 while IUC reviews are slowly sorted out. +- UPDATED existing JBrowse1.16.11 code to JBrowse 2.10.0 +- was working well enough for VGP when previous PR discovered + - too late to backport all the fixes + - working default session and some other ideas copied instead. +- seems to work well with defaults. +- need to document and implement track settings by running the browser locally. +- works well enough to be useful in workflows such as TreeValGal. +- JB2 seems to set defaults wisely. +- not yet ideal for users who need fine grained track control. +- synteny (paf + reference) now working +- rehomed at https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 while IUC reviews are slowly sorted out. Wrapper License (MIT/BSD Style)