(referring to this: https://jbrowse.org/docs/tutorial.html)
Hello,
I am using maker2jbrowse with this 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
I think I know what it could be...will have to check into it
for the maker2jbrowse thing
which is already something :) although not exactly what I was expecting! :)
@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?
Any idea what that’s about?
storeClass: JBrowse/Store/SeqFeature/BgzipIndexedFasta
I figured the adapter would just “figure it out” :-)
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 :)
is there an issue with it?
confirmed that the ip in aws console == ping covid19.jbrowse.org ip
i dunno whats goin on with that instance though
it says it is running now
but no ping
no http access
…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.
…and it’s back. Yay, I don’t actually have to fix anything today.
hello, not related to gbrowse
could anyone give an alternate to CMap (http://gmod.org/wiki/CMap#Documentation)
could anyone give an alternate to CMap (http://gmod.org/wiki/CMap#Documentation)
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.
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
$ 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
@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.
@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.