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  • Nov 19 02:58
    cmdcolin commented #1556
  • Nov 19 02:56
    cmdcolin commented #1556
  • Nov 19 02:55

    cmdcolin on uniqueID_remove_gff3tabix

    Remove uniqueID from featureData (compare)

  • Nov 18 06:49
    Jungal10 commented #1556
  • Nov 17 20:36
    cmdcolin commented #1556
  • Nov 17 20:33
    cmdcolin commented #1556
  • Nov 13 19:04
    jrobinso opened #118
  • Nov 13 18:22
    Jungal10 commented #1556
  • Nov 13 18:21
    Jungal10 commented #1556
  • Nov 13 15:41
    cmdcolin commented #1556
  • Nov 13 06:24
    Jungal10 commented #1556
  • Nov 12 22:59
    cmdcolin commented #1556
  • Nov 12 22:39
    Jungal10 edited #1556
  • Nov 12 22:38
    Jungal10 opened #1556
  • Nov 12 21:52
    cmdcolin commented #1555
  • Nov 12 21:47
    cmdcolin commented #1555
  • Nov 12 21:46
    cmdcolin commented #1555
  • Nov 12 17:43
    GFJHogue opened #1555
  • Nov 10 00:38
    jrobinso commented #79
  • Nov 09 22:57
    cmdcolin commented #67
Colin Diesh
@cmdcolin
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
ok
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?
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

image.png
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:
image.png
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
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 :)

Scott Cain
@scottcain
@cmdcolin covid19.jbrowse.org is down. Can you please give it a swift kick? Thanks
Colin Diesh
@cmdcolin
@scottcain i rebooted it awhile ago and it did not come back up
is there an issue with it?
Scott Cain
@scottcain
:shrug: I don’t know anything about how it’s set up, but I don't think anything has changed recently.
Colin Diesh
@cmdcolin
i hit the reboot on it
confirmed that the ip in aws console == ping covid19.jbrowse.org ip
Ian Holmes
@ihh
is there a reason it needs to be an EC2 node and not just a static site?
Scott Cain
@scottcain
Nope. I’m not sure when that decision was made. I had a docker container so somebody (perhaps @nathandunn ) decided to just run an EC2 with the docker running on it. I can set up a static site fairly easily.
Colin Diesh
@cmdcolin
prolly upload the data to s3
i dunno whats goin on with that instance though
it says it is running now
but no ping
no http access
Scott Cain
@scottcain
That’s the (not really) funny thing: all the data are either on S3 already or being served from somewhere else (UCSC).
…although I do need to update the data, and I didn’t really want to do that today, but I also don’t want to do a half-assed job setting up a static site but not updating the data.
Scott Cain
@scottcain
Also, it turns out I have ssh access to the covid19 machine, so I’ll try to fix it.
…and it’s back. Yay, I don’t actually have to fix anything today.
git-u0
@git-u0
hello, not related to gbrowse
could anyone give an alternate to CMap (http://gmod.org/wiki/CMap#Documentation)
Scott Cain
@scottcain
There are not many good alternatives. The closest thing I know of is Tripal MapViewer (example https://www.cottongen.org/tools/mapviewer). While it is a good tool, the problem is that it requires that you also have tripal, which is a whole thing. I also heard a rumor a few years ago about somebody working on a JavaScript implementation of CMap but I don’t know if it ever saw the light of day. I’ll look around tomorrow morning when I’m at my desk.
git-u0
@git-u0
Thank you for the info, i was trying to install CMap and had some issues that's why i asked for alternates. The following is the error,
$ perl Build.PL :ran OK
$ ./Build
output,
Building cmap
option backlink does not take an argument
./Build: invalid arguments
why such an error when there are no arguments given for Build