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    codecov[bot] commented #119
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    codecov[bot] commented #15
  • Nov 24 23:42
    codecov[bot] commented #61
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
Scott Cain
@scottcain
@git-u0 Wow, CMap is very old and hasn’t been maintained in a long time; I’m not sure the mailing list even exists any more. One thing you might try is installing an older linux system and use it’s package manager to install as many of the perl modules as you can. It wouldn’t be very secure (since it wouldn’t have gotten security updates in a while) but it might work. I’m thinking Ubuntu 12.04 or 14.04 might do the trick.
Robert Buels
@rbuels
@scottcain how big a market do you think a jb2 cmap plugin would have?
Scott Cain
@scottcain
@rbuels cmap is still pretty popular in the plant community, but Tripal is also pretty popular, and it has a cmap like plugin. Also, the cmap-js thing I mentioned above is still under active development (in react), so it’s possible that there might be the posibility of cross pollination there. I’m waiting to hear back if they have a repo I can share with people.