Scott Cain scottcain

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BioPerl Generic Model Organism Database Project gmodevohack
scottcain commented on issue WormBase/website#3555
Scott Cain

Hi Wolfgang (@wm75), I think you might not be aware of the SequenceDumper plugin, since it isn't currently available in the WormBase GBrowse instan…

scottcain commented on issue WormBase/website#3613
Scott Cain

I was under the impression that these changes just get the 247 gff back to the way they "should" be (which is to say, like 246); or is there someth…

scottcain commented on issue WormBase/website#3555
Scott Cain

So the problem is fairly deep in BioPerl (in the mysql adaptor for Bio::DB::SeqFeature::Store); I imagine it is possible for me to fix it, but it w…

scottcain commented on issue WormBase/website#3555
Scott Cain

Oh, I didn't realize that download track data plugin is activated. I'm not sure it should be because I'm not sure if it's still supported. Executin…

scottcain commented on pull request WormBase/website#3652
Scott Cain

OK, then this pull request should be rejected and bug #3550 should be marked closed (after the database has been rebuilt and it's been verified tha…

scottcain commented on pull request WormBase/website#3652
Scott Cain

When I got this: ftp://ftp.wormbase.org/pub/wormbase/releases/WS246/species/c_elegans/PRJNA13758/c_elegans.PRJNA13758.WS246.annotations-processed.g…

scottcain opened pull request WormBase/website#3652
Scott Cain
the 246 gff lost the "locus" attribute for gene:landmark features, but h...
1 commit with 1 addition and 1 deletion
Scott Cain
  • Scott Cain c4ad4d6
    the 246 gff lost the "locus" attribute for gene:landmark features, bu…
scottcain commented on issue WormBase/website#3555
Scott Cain

I wonder if this was for C. japonica, as the 246 mysql database was having problems. It seems to be working now.

Scott Cain
Hi there! The "Download Track data" f...
scottcain commented on issue WormBase/website#3578
Scott Cain

This is fixed in the mysql database c_japonica_PRJNA12591_WS246. It's unclear to me if it needs to be fixed in the 246 database as well, or if this…

scottcain commented on issue WormBase/website#3578
Scott Cain

I think this a problem with the mysql database. The primary GBrowse database for C. japonica is mostly empty: the database named c_japonica_PRJNA12…

Scott Cain
Jbrowse track labels
scottcain commented on issue WormBase/website#3622
Scott Cain

The new, better labeling has been commited :-)

scottcain commented on issue WormBase/website#3624
Scott Cain

So part of what is going on with let-7 is that GBrowse doesn't know what to do with features of type 'miRNA_primary_transcript', but it "knows" the…

scottcain commented on issue WormBase/website#3624
Scott Cain

I was planning on setting up my own GBrowse instance to work with this data, so I'll do that today and look into why data seems to be getting misse…

scottcain commented on issue WormBase/website#3622
Scott Cain

Is this better? I'd say this is better than what currently happens in GBrowse: (as an aside, it looks like I have the colors backwards--I'll fix …

scottcain commented on issue WormBase/website#3622
Scott Cain

In this instance, it looks like it would make more sense just to suppress the isoform name altogether, unless in this track there are different iso…

scottcain commented on issue GMOD/jbrowse#556
Scott Cain

I missed that collapsedCategories isn't an option yet for the faceted selector--I think implementing that would be a good idea. I'm also thinking t…

scottcain commented on issue GMOD/jbrowse#556
Scott Cain

I was unaware of selectableFacets--I will definitely use that to take out the "citation" from the left column--I had a request to do that too! I ac…

Scott Cain
A way to shorten entries in faceted track selector
Scott Cain
In faceted track selector option for number of tracks on the right
Scott Cain
Make left column in faceted selector resizable
scottcain opened pull request WormBase/website#3571
Scott Cain
fixing a minor typo; while this typo in the production conf doesn't appe...
1 commit with 1 addition and 1 deletion
Scott Cain
  • Scott Cain ed32330
    fixing a minor typo; while this typo in the production conf doesn't a…