GMOD/jbrowse

JBrowse 1 maintenance and issues

Colin Diesh

@cmdcolin

@scottcain good question

primer stuff always makes my brain go blank :) should find some good answers for that tho

the more detail you can get from the user the better probably...and even better to try to roll the workflow into jbrowse itself

one option is https://github.com/cmdcolin/JBrowse-PrimerDesigner

Keiran Raine

@keiranmraine

Is there a plugin for the alignments track in JBrowse(1) that has similar functionality to the the methylation option on JBrowse2?

Colin Diesh

@cmdcolin

Jb2 feature is not backported to jb1 afaik

The code is there in jb2 though if anyone wanted to do so:)

Keiran Raine

@keiranmraine

No worries, I didn't think so. We're close to the point where we need to upgrade the OS on the server where JBrowse lives so considering the switch over to JB2... although have no idea when I'll find the time to port https://github.com/cancerit/proportionalmultibw

Yun Zhang

@yzhang2168

Hi, Yun from the Virus Pathogen Resource. We have some segmented viruses like influenza virus has 11 segments. I wonder if there are options to visualize all segments together? Or it has to 1 segment per Jbrowse window?

Colin Diesh

@cmdcolin

@yzhang2168 in jbrowse 2 you can display multiple chromosomes e.g. full human genome at the same time

In jbrowse 1 it is not possible just one chromosome/config at a time. So if your viruses are in 11 diff configs jb2 may be a good option

Yun Zhang

@yzhang2168

@cmdcolin cool. Do you have an example that I can take a look at?

Yun Zhang

@yzhang2168

one major difference between my use case and multiple chromosomes is that each segment has its own annotation tracks, so segment 1 has its CDS and other feature tracks, segment 2 has a different set of features, etc.

Colin Diesh

@cmdcolin

see jbrowse.org it is now based on jbrowse 2 primarily

Scott Cain

@scottcain

and the addTracks section looks like this:

[{
"label":"Primers",
"type":"JBrowse/View/Track/CanvasFeatures",
"store":"url",
"subParts":"match_part",
"glyph":"JBrowse/View/FeatureGlyph/Segments",
"style":{
"color":"red",
"strandArrow":true}
}]

Colin Diesh

@cmdcolin

probably not, i would use color or something to indicate strand

jbrowse 2 actually does this though, see https://jbrowse.org/code/jb2/v1.5.1/?config=test_data%2Fvolvox%2Fconfig.json&session=share-gnqrjBouT_&password=G6r30

fingerprinted bac ends is a feature with subfeatures pointing at each other

Scott Cain

@scottcain

If there were a way to add features via url, I would totally suggest to this user that they use jbrowse_img.

Scott Cain

@scottcain

(oh, and support for nclist)

Scott Cain

@scottcain

also, can’t really color by strand when adding via url, since js isn’t allowed, right?

Scott Cain

@scottcain

Interesting (sort of) error in my WB protein browser: SyntaxError: Unexpected token ')' at Object.dojo.fromJson (0.bundle.js:8) at 1.bundle.js:1… in this page: https://staging.wormbase.org/tools/protein_schematic/?data=data%2Fc_elegans_PRJNA13758&loc=F11C7.3%3A1..424&tracks=Exon%20boundaries%2Cseg%2Csignalp%2CMotifs

Is this more likely to be a json/track data problem (which seems likely to me) or a js problem? Both were built today (jbrowse from the dev branch).

Well, maybe it is a js problem, since it happens with a different data set, so unless it’s broken in the same way …

… on the other hand, there have been no commits to the dev branch in the last several months. Maybe I’ll just rebuild the docker container.

… and probably most likely, there is a problem with the config and/or callbacks. Anybody enjoy me live messaging my debugging (from a plane, where everybody knows your brain don’t work so good)

Scott Cain

@scottcain

Ha, it was a docker build problem. Did it again (without changing anything) and now it magically works.

Scott Cain

@scottcain

Does JB 1 support adding a gff/tabix track via url? (yes, I will go looking for docs soon, but I’m looking for a preview of what I’ll find :-)

Colin Diesh

@cmdcolin

@scottcain see the combo addstore addtrack examples here https://jbrowse.org/docs/url_strings.html#addstores

Scott Cain

@scottcain

👍 hopefully I’ll get back to this today :-)

Colin Diesh

@cmdcolin

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Caroline Bridge

@carolinebridge-oicr

nice to see colin's new cat making contributions so young

Colin Diesh

@cmdcolin

that was indeed cat

Scott Cain

@scottcain

lol

Matt

@mjy

Debugging an "old" docker file.

RUN wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-4.6.14-Linux-x86_64.sh -O ~/miniconda.sh && \
    /bin/bash ~/miniconda.sh -b -p /conda/ && \
    rm ~/miniconda.sh

Is there a preferred miniconda repo that works with 1.16.11, so that I could at least eliminate that as an issue?

Colin Diesh

@cmdcolin

@mjy what is the issue?

i don't have much experience with docker,it might be that conda is not needed perhaps

Matt

@mjy

@cmdcolin a container I've used for the past while no longer builds. However I can't be certain if it's a Docker update (Mac) or M1 related, or another issue. I basically have a very minimal dockerfile poached from somewhere that uses conda (mini) to install jbrowse.

https://pastebin.com/F9n9LrFQ for the container for those curious.

Scott Cain

@scottcain

@mjy do you get any useful messages during the build that might point at what the problem is? I found the Dockerfile that uses miniconda to be difficult to work with when I got started with docker a little over a year ago, which is why I built my own “build” base images (that are on docker hub) and then built both GFF processing containers and server containers off of those for various projects.

Matt

@mjy

I've looked at the conda tracker and found similar issues from others:

 > [gage_jbrowse 6/8] RUN conda install -y --override-channels --channel iuc --channel conda-forge --channel bioconda --channel defaults jbrowse=1.16.:
#12 2.015 Collecting package metadata (current_repodata.json): ...working... done
#12 67.67 Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.
#12 89.45 Solving environment: ...working... failed with repodata from current_repodata.json, will retry with next repodata source.
#12 113.5 Collecting package metadata (repodata.json): ...working... Killed
------
failed to solve: rpc error: code = Unknown desc = executor failed running [/bin/sh -c conda install -y --override-channels --channel iuc --channel conda-forge --channel bioconda --channel defaults jbrowse=1.16.]: exit code: 137

I'm more or less planning to do the same and build my own base nginx image, am aware of other jbrowse docker examples to reference in doing so.

Scott Cain

@scottcain

Yeah, I know essentially nothing about conda. I think @hexylena may know more.

Helena Rasche

@hexylena:matrix.org

[m]

Hello! I am here :)

for conda installation of jbrowse ok, one sec

those are exactly the channels we pull from @mjy , odd that it's failing

but I'm seeing similar output locally.

mamba can solve it though it seems! If that's not a huge impediment to your workflow, just conda install mamba and mamba install jbrowse=1.16.11 or so (with same channel overrides if those aren't the defaults)

conda's solver is ... difficult sometimes.

Matt

@mjy

@hexylena:matrix.org thank you. Exactly the feedback I needed.

For reference, I modified the dockerfile lines like so:

RUN conda install -c conda-forge mamba

RUN mamba install -y --override-channels --channel iuc --channel conda-forge --channel bioconda --channel defaults jbrowse

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