Hello, I am testing to replace jbrowse with mouse data, but the tbi of the mouse gff3 file is always wrong here. I don't know what is wrong. I would like to ask you about the index. Do you have any mouse data to provide? ? thanks

[ouyang-lang]

Hello, I am testing to replace jbrowse with mouse data, but the tbi of the mouse gff3 file is always wrong here. I don't know what is wrong. I would like to ask you about the index. Do you have any mouse data to provide? ? thanks

The data I use is the ensemble version, and my error is:
Error: problem decompressing block: incorrect gzip header check
Is my decompression method wrong?

[cmdcolin]

Generally to prepare a GFF3 tabix file you can use

gt gff3 -sortlines -tidy -retainids file.gff > file.sort.gff
bgzip file.sort.gff
tabix file.sort.gff.gz

then put both file.sort.gff.gz and file.sort.gff.gz.tbi in your data directory

Then make in your config file

{
"type":"CanvasFeatures",
"urlTemplate":"file.sort.gff.gz",
"label":"mytrack",
"storeClass":"JBrowse/Store/SeqFeature/GFF3Tabix"
}

If it continues to have issues, you might have issues with your server. JBrowse does NOT like the server to return the HTTP header "Content-Encoding: gzip" for tabix files.

Xref similar thread and FAQ
#1512

https://jbrowse.org/docs/faq_troubleshooting.html#what-is-the-error-invalid-bgzf-header-on-my-vcf-files

One possible way to fix could be to give your files a random extension if your server is doing this based on file extension e.g.

mv file.sort.gff.gz file.sort.gff.blah
mv file.sort.gff.gz.tbi file.sort.gff.blah.tbi

{
"type":"CanvasFeatures",
"urlTemplate":"file.sort.gff.blah",
"label":"mytrack",
"storeClass":"JBrowse/Store/SeqFeature/GFF3Tabix"
}

[ouyang-lang]

Thanks, I have solved the problem, thanks a lot

[cmdcolin]

Great :) if you did anything different to solve feel free to post how, definitely this is an issue that comes up fairly frequently

[ouyang-lang]

Hello, it is solved by the method you said, but I use GUN for sorting
(grep ^"#" data/volvox.gff3; grep -v ^"#" data/volvox.gff3 | grep -v "^$" | grep "\t" | sort -k1,1 -k4,4n) > data/volvox.sorted.gff3

[cmdcolin]

excellent, good to know!

[ouyang-lang]

Is jbrowse incompatible with vue, why can't my project start when I put it in vue?

[cmdcolin]

jbrowse 1 can be a little awkward to put into a react/vue app. I demonstrated using jbrowse 1 here in a react app which might be somewhat similar to vue https://github.com/cmdcolin/jbrowse_in_react_app

also, you can consider jbrowse 2. a user demonstrated how to use it in a vue app here GMOD/jbrowse-components#2930

[ouyang-lang]

ok, i'll try, i'm a newbie and i'm using JBROWSE2 too

[ouyang-lang]

thanks very much

[ouyang-lang]

hello，I used the code of this vue, but he kept reporting such an error. I tried many solutions, but I couldn't solve it. I would like to know how the people who used it successfully in vue at that time solved this problem?

my error：
Module parse failed: Unexpected token (131:21)
You may need an appropriate loader to handle this file type.
| }
| return depths.map(d => {
| return { ...d, score: (d.score * stats.lineCount) / totalSize };
| });
| }

[ouyang-lang]

[cmdcolin]

might close for now. the above build errors stem from not running setup.sh properly perhaps, or somehow the yarn.lock file being ignored. the current babel setup, being quite old, can't even handle spread syntax