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GMOD / JBrowseR

R interface to the JBrowse 2 Linear Genome View.
https://gmod.github.io/JBrowseR/
Apache License 2.0
35 stars 3 forks source link

Custom browser with ensembl genomes #9

Open RichardJActon opened 2 years ago

RichardJActon commented 2 years ago

I've been testing out JBrowseR, (thanks for developing it, it looks great for several use-cases I have), and I've been having trouble setting up a custom browser.

I copied your example from the custom browser tutorial and swapped out the example genome for the build I'm interested in using:

ftp://ftp.ensembl.org/pub/release-91/fasta/caenorhabditis_elegans/dna_index/Caenorhabditis_elegans.WBcel235.dna.toplevel.fa.gz

This did not work, the assembly shows up in the drop-down but there is an indefinite loading circle with the open and show all regions in assembly buttons greyed out.

I'm note sure if it would be expected to work over ftp as I can't remember if this supports Byte serving as you mentioned in the creating URLs guide:

https://gmod.github.io/JBrowseR/articles/creating-urls.html

So I tried downloading the ensmbl data to a local directory and serving it with serve_data but got the same result

Any idea what I'm missing?

Just tried running the example on my local machine with Rstudio desktop and it worked with serve_data. So I think the issue with serve_data was arising from something to do with the network setup to I have access the remote RStudio server instance running on my workstation. I think maybe the local server created is not accessible to the other one the shiny app is running in for some reason

cmdcolin commented 2 years ago

Thanks for trying it out!

Just tried running the example on my local machine with Rstudio desktop and it worked with serve_data. So I think the issue with serve_data was arising from something to do with the network setup to I have access the remote RStudio server instance running on my workstation. I think maybe the local server created is not accessible to the other one the shiny app is running in for some reason

Yes I think you got the right idea with serve_data...it would be ideal to make serve_data be a little easier to use probably either being more transparent or more obvious. Glad you got it figured out locally. If you figure out something for the server setup let us know ...not sure I have access to that setup myself

elliothershberg commented 2 years ago

Hi @RichardJActon , thanks for opening this issue. I didn't see this issue until now, but your intuition here is correct. The serve_data() function starts up a small local http server, and if you are using RStudio remotely, it won't have access to those files being served.

Have you been able to find a workaround that works for the use cases you are thinking about using JBrowseR for?

RichardJActon commented 2 years ago

Hi @elliothershberg, apologies for the delay in replying. I've not figured out a work around. My setup is a little odd I'm running RStudio server in a docker container on my workstation that I usually access via ssh port forwarding to my box at home. However stuff like running a shiny app in RStudio that also creates a local server does work when I'm using it like this. I'm not familiar enough with the implementation details of either to say why this works for a Shiny app and not serve_data()