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
line wrap: on
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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)