GMOD/jbrowse

JBrowse 1 maintenance and issues

Colin Diesh

@cmdcolin

(i gotta watch movie now but lemme know if anything comes up)

David Eccles (gringer)

@gringer

Seems to just be those two tracks; other tracks where I've updated the underlying files aren't displaying the same issues

Scott Cain

@scottcain

@cmdcolin from Terence at NCBI: "Thanks again for the report. We’ve made some changes to our web server so that the “Content-Type: application/x-bam” header should be consistently returned. It looks like this has fixed the problem for IGV. Does that fix the JBrowse problem as well?"

Colin Diesh

@cmdcolin

should work now ya

Colin Diesh

@cmdcolin

i will check shortly but quickly looking at a previous example where it failed it is no longer returning content-encoding:gzip which is what we wanted

send terence a big thanks :]

Scott Cain

@scottcain

I sent him a response thanking him and his team and said it almost certainly fixed the problem but I would let him know if we run into anything else.

Scott Cain

@scottcain

@cmdcolin I think the wigglehighlighter plugin may have stopped working recently. At https://staging.wormbase.org/tools/genome/jbrowse-simple/?data=data%2Fc_elegans_PRJNA13758&loc=II%3A1..1758000&tracks=ALY-2%20Combined%20(GFP%20ChIP)_%20ALY-2_GFP_L2%20w%20peaks I get an error message like TypeError: s.config.highlightColor is not a function TypeError: s.config.highlightColor is not a function Is that more likely something I did, or something that happened in JBrowse core?

The bigwig and bigbed files both continue to exist. The bigbed has Content-Encoding: bzip2 and Content-Type: binary/octet-stream

Colin Diesh

@cmdcolin

might have changed a little bit

there was a user coding and iterating the wigglehighlighter codebase

lemme check

Scott Cain

@scottcain

Oh, and in case it matters, I’m using the dev branch for jbrowse.

Colin Diesh

@cmdcolin

could try to pull from wigglehighlighter master

it has an update

Scott Cain

@scottcain

Highlighting is back, but it now seems to what to label the bigbed features (I’m guessing), like this https://staging.wormbase.org/tools/genome/jbrowse-simple/?data=data%2Fc_elegans_PRJNA13758&loc=II%3A127995..191994&tracks=ALY-2%20Combined%20(GFP%20ChIP)_%20ALY-2_GFP_L2%20w%20peaks

I’m guessing I can supress that somehow

Colin Diesh

@cmdcolin

I think you have showLabels: true on there

or actually

can set showLabels:false

i guess its true by default

i could switch it if it seems easier

Scott Cain

@scottcain

Interesting—I don’t think the labels were there before. Anyway, making it false by default would be a lot easier since I have quite a few tracks, and I suspect most people would want it off in a context like this anyway.

Colin Diesh

@cmdcolin

ill just switch it off

Scott Cain

@scottcain

👍

Colin Diesh

@cmdcolin

should be updated again

Scott Cain

@scottcain

Looks good; thanks @cmdcolin

Colin Diesh

@cmdcolin

very good

Scott Cain

@scottcain

In the indexed file tutorial, it doesn’t mention bgziped fasta as a option. I’m guessing those are supported though, right? So I should be good if I supply .gz, .gz.fai and .gz.gzi files, ya?

(referring to this: https://jbrowse.org/docs/tutorial.html)

Garrett Stevens

@garrettjstevens

Should work, and you can use faiUrlTemplate and gziUrlTemplate if it doesn't pick them up automatically from the urlTemplate

Scott Cain

@scottcain

👍

Domenico Simone

@domenico-simone

Hello,

I am using maker2jbrowse with this GFF:

https://github.com/domenico-simone/jbrowse_mini_test/blob/test/input_data_201021/all.batches.wseqs.annotation.test.2.clean.gff

This is an excerpt of the settings I'm using in the script:

my %commands = (

    #MAKER anotations
    gene            => [ '--key' => "Gene spans",
                         '--className' =>  'feature',
                         '--type' => 'gene:maker',
                         '--noSubfeatures'
                       ],
    maker           => [ '--key' => "Transcripts",
                         '--className' => 'transcript',
                         '--subfeatureClasses' => '{"exon": "exon", "CDS": "CDS", "five_prime_UTR": "five_prime_UTR", "three_prime_UTR": "three_prime_UTR"}',
                         '--type'  => 'mRNA:maker',
                         '--nameAttributes' => 'name,alias,id,note,dbxref,ontology_term'
                       ],

The building process works fine, but when I open the genome browser the "Gene spans" track is not loaded (see attached figure)

am I missing anything from the configuration?

Thank you,

Domenico

Colin Diesh

@cmdcolin

@domenico-simone I found this error too recently GMOD/jbrowse#1548

I think I know what it could be...will have to check into it

Domenico Simone

@domenico-simone

Thank you @cmdcolin, I'm following the thread on github

Colin Diesh

@cmdcolin

added a small pr...

for the maker2jbrowse thing

Domenico Simone

@domenico-simone

Hi @cmdcolin thank you! this is what I get now:

which is already something :) although not exactly what I was expecting! :)

Colin Diesh

@cmdcolin

ah right. i guess technically the gene spans maybe used to be just a single box covering the gene region but maybe it automatically loads individual transcripts now

Scott Cain

@scottcain

@cmdcolin My indexed fasta is throwing a 416 (! that’s a new one to me) error: http://dev.wormbase.org:9018/tools/genome/jbrowse/?data=data%2Fc_elegans_PRJNA13758&loc=III%3A9992015..9992306&tracks=AnaBlast%20sORFs%2CsORF.org%2CDNA%2Cindexed%20DNA&highlight=
Any idea what that’s about?

Colin Diesh

@cmdcolin

ur gonna wanna set

storeClass: JBrowse/Store/SeqFeature/BgzipIndexedFasta

Scott Cain

@scottcain

👍

I figured the adapter would just “figure it out” :-)

Domenico Simone

@domenico-simone

ah right. i guess technically the gene spans maybe used to be just a single box covering the gene region but maybe it automatically loads individual transcripts now

@cmdcolin I think you're right. So far, in my case showing only the transcripts is ok. However, if this could be fixed it would be great :)

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