Re: [Gmod-ajax] Problems installing GWAS viewer plugin

[Hans Vasquez-G. <hva...@un...>]

Hi Colin,

Thank you for the feedback. I updated the displayId for the two tracks to be unique.  Now the example data one is working. However, our test file isn't working.

Here is an excerpt from the file. I need to update the calculations for neg_log column because it isn't correct, but I think it should be still enough information to test the GWAS plugin with our own files.
chromosome  base_pair_location      p_value     neg_log
10    82228 0.430992    2.69769
10    82636 0.333756    2.15653
10    85696 0.838472    6.89401
10    86828 0.42009     2.63081
10    88007 0.924451    8.40332
10    88058 0.924451    8.40332
10    89716 0.363215    2.30789
10    89913 0.925755    8.42859
10    91246 0.873263    7.46901


With the config.json excerpt here:
{
  "type": "FeatureTrack",
  "trackId": "gwas_track_parkinsons",
  "name": "GWAS Parkinsons",
  "category": ["Annotation"],
  "assemblyNames": ["hg19"],
  "adapter": {
    "type": "BedTabixAdapter",
    "scoreColumn": "neg_log",
    "bedGzLocation": {
      "uri": "GCST011038_buildGRCh37.4col.tsv.gz"
    },
    "index": {
      "location": {
        "uri": "GCST011038_buildGRCh37.4col.tsv.gz.tbi"
      },
      "indexType": "TBI"
    }
  },
  "displays": [
    {
      "displayId": "gwas_display2",
      "type": "LinearManhattanDisplay"
    }
  ]
}


I created the index with the following command:
tabix -0 -b 2 -s 1 -S 1 -e 2 -f GCST011038_buildGRCh37.4col.tsv.gz

If you need the URL for this jbrowse2 installation for testing, I could provide it to you directly.

Thank you for the advice.

All the best,
-Hans
________________________________
From: Colin <col...@gm...>
Sent: Wednesday, May 24, 2023 3:27 PM
To: Hans Vasquez-Gross <hva...@un...>
Cc: gmod-ajax <gmo...@li...>; Jeremiah B Reyes <jr...@un...>
Subject: Re: [Gmod-ajax] Problems installing GWAS viewer plugin


[EXTERNAL EMAIL]

Hi there, the error is saying there are two tracks with the same displayId essentially, but the displayId needs to be unique, so you can change the track config to say gwas_viewer1 and gwas_viewer2 (or any random set of unique strings)

Hope that helps!
-Colin

On Wed, May 24, 2023, 3:57 PM Hans Vasquez-Gross <hva...@un...<mailto:hva...@un...>> wrote:
Hello All,

I believe I successfully configured the addition of the GWAS plugin within the config.json file.  However, when I try to load the track with the example data, I get the following error:


Error: [mobx-state-tree] Cannot resolve a reference to type 'LinearManhattanDisplayConfigurationSchema' with id: 'gwas_display' unambigously, there are multiple candidates: /jbrowse/tracks/91/displays/0, /jbrowse/tracks/92/displays/0

How would I go about troubleshooting this error? Any advice would be greatly appreciated.

Thank you,
-Hans


--



[signature_998258195]

Hans Vasquez-Gross, Ph.D

Bioinformatics Scientist,
Nevada Bioinformatics Center

https://www.unr.edu/bioinformatics

hva...@un...<mailto:hva...@un...>

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