v2.8.0 release announcement (#4049)

plugins/bed/src/BedpeAdapter/BedpeAdapter.ts

@@ -42,7 +42,7 @@ export function featureData(
     start: start1,
     end: end1,
     refName: ref1,
-    ALT: [ALT], // it's an array in VCF
+    ...(ALT ? { ALT: [ALT] } : {}), // it's an array in VCF
     strand: strand1,
     name,
     ...rest,

website/docs/quickstart_web.md

@@ -20,9 +20,6 @@ import config from '../docusaurus.config.json'
 - [tabix](http://www.htslib.org/doc/tabix.html) installed e.g.
   `sudo apt install tabix` and `brew install htslib`, used for creating tabix
   indexes for BED/VCF/GFF files
-- (optional) [`genometools`](http://genometools.org/) installed e.g.
-  `sudo apt install genometools` or `brew install brewsci/bio/genometools` used
-  for sorting GFF3. can use grep and sort instead of `genometools` also
 
 ## Installing the JBrowse CLI
 
@@ -227,22 +224,16 @@ jbrowse add-track file.bw --load copy --out /var/www/html/jbrowse
 
 ### Adding a GFF3 file with GFF3Tabix
 
-To load a GFF3 file, we can sort and index it with tabix, make sure you have
-[GenomeTools](http://genometools.org/) (to install can use
-`sudo apt install genometools`).
-
 ```bash
-gt gff3 -sortlines -tidy -retainids yourfile.gff > yourfile.sorted.gff
-bgzip yourfile.sorted.gff
+jbrowse sort-gff yourfile.gff | bgzip > yourfile.sorted.gff.gz
 tabix yourfile.sorted.gff.gz
 jbrowse add-track yourfile.sorted.gff.gz --load copy
 ```
 
-As an alternative to `gt gff3 -sortlines`, use `awk` and GNU `sort`, as follows:
+Note: the `jbrowse sort-gff` command just automates the following shell command
 
 ```bash
-(grep "^#" in.gff; grep -v "^#" in.gff | sort -t"`printf '\t'`" -k1,1 -k4,4n) | bgzip > file.sorted.gff.gz;
-tabix file.sorted.gff.gz
+(grep "^#" in.gff; grep -v "^#" in.gff | sort -t"`printf '\t'`" -k1,1 -k4,4n)  > sorted.gff;
 ```
 
 This command comes from the

website/release_announcement_drafts/v2.8.0.md

@@ -0,0 +1,22 @@
+This release improves support for BEDPE and arc rendering of structural
+variants.
+
+It also adds a new CLI command called `jbrowse sort-gff` that intends to help
+simplify the loading of GFF tabix tracks.
+
+Usage:
+
+```
+jbrowse sort-gff yourfile.gff | bgzip > yourfile.sorted.gff.gz
+tabix yourfile.sorted.gff.gz
+jbrowse add-track yourfile.sorted.gff.gz --load copy --out /var/www/html/jbrowse2
+```
+
+The jbrowse CLI tool can load BEDPE files with simply
+`jbrowse add-track yourfile.bedpe` (or, optionally gzipped e.g.
+yourfile.bedpe.gz)
+
+![](https://user-images.githubusercontent.com/6511937/281789167-aef6ccd2-c7e4-444e-b213-f3876fedabf9.png)
+
+Screenshot showing the same data rendered as both a BEDPE file and VCF file with
+different variant types (`<DUP>, <DEL>, <INV>, <TRA>`)