search

GMOD / jbrowse-components

Source code for JBrowse 2, a modern React-based genome browser
https://jbrowse.org/jb2
Apache License 2.0
205 stars 61 forks source link

JBrowse issue #4490

Closed zmt11 closed 2 months ago

zmt11 commented 2 months ago

I got this error from JBrowse, here is the stack trace:

Error: file ("ASM2152768v1.genome.fasta") was opened locally from a previous session. To restore it, go to track settings and reopen the file

../../../packages/core/util/io/index.ts:64:13 (at h ()
../../../plugins/sequence/src/IndexedFastaAdapter/IndexedFastaAdapter.ts:52:29 (at f.setupPre ()
../../../plugins/sequence/src/IndexedFastaAdapter/IndexedFastaAdapter.ts:67:26 (at f.setup ()
../../../plugins/sequence/src/IndexedFastaAdapter/IndexedFastaAdapter.ts:37:34 (at f.getRegions ()
../../../packages/core/assemblyManager/assembly.ts:508:18 (at)
../../../packages/core/assemblyManager/assembly.ts:392:15 (at async Object.loadPre ()
JBrowse 2.12.3
cmdcolin commented 2 months ago

this was also sent to our jbrowse2@berkeley.edu email. my response there :)

"The admin-server has some specific limitations that can be a little confusing

Specifically, it expects you to only input URLs to files (which are then written directly to the config.json file)

It does not have a notion of opening local files from your computer, which would need an "uploader" to put the files into the right folder

I would generally recommend using the command line ("CLI") to get your instance setup, using the "jbrowse add-assembly" command to add your assembly

You can run e.g.

samtools faidx yourfile.fa jbrowse add-assembly yourfile.fa --out /path/to/jbrowse/folder --load copy

And it will create a config.json in the /path/to/jbrowse/folder folder, and copy the yourfile.fa and yourfile.fa.fai file there

Then you can continue to add tracks as needed. The admin-server can be useful when you want to perform customizations to the "Settings"/config editor of the tracks, as these will be automatically saved to the disk, but for adding new tracks and assemblies it is a little trickier as you found here"

cmdcolin commented 2 months ago

might close for now, email thread had a positive outcome :)