Closed wjwei-handsome closed 3 years ago
This message is shown in every jbrowse home page. If you pass some variables informing where the data is, it should work fine.
Try this:
http://1.14.226.153/jbrowse/?data=data%2FAAA%20aaa&tracks=ref_seq%2Cgene%2Ctranscripts%2CCDS
This message is shown in every jbrowse home page. If you pass some variables informing where the data is, it should work fine.
Try this:
http://1.14.226.153/jbrowse/?data=da
This message is shown in every jbrowse home page. If you pass some variables informing where the data is, it should work fine.
Try this:
http://1.14.226.153/jbrowse/?data=data%2FAAA%20aaa&tracks=ref_seq%2Cgene%2Ctranscripts%2CCDS
Thanks for your answers, but my error still exists
I try to GET the url : http://1.14.226.153:8000/api/jbrowse/refSeqs.json?soType=chromosome&organism=AAA%20aaa , and it responded normally when i turn on the Django server. I am still confused about this.
The file refSeqs.json is generated by the API, so it depends on the Django server to be running. But I couldn't figure out yet why JBrowse can't load it.
The file refSeqs.json is generated by the API, so it depends on the Django server to be running. But I couldn't figure out yet why JBrowse can't load it.
Thank you for your reply. Machado is a very good Django framework. I plan to use it as part of my database. If the Jbrowse problem cannot be solved, I think I can try without using the REST framework.
I recommend you load the reference data (the chromosomes) from the .fasta file. It'll be faster that way.
https://machado.readthedocs.io/en/latest/jbrowse.html#use-reference-from-fasta-file-optional
Once the reference track is setup, you should be able to visualize the features from the database.
I recommend you load the reference data (the chromosomes) from the .fasta file. It'll be faster that way.
https://machado.readthedocs.io/en/latest/jbrowse.html#use-reference-from-fasta-file-optional
Once the reference track is setup, you should be able to visualize the features from the database.
Thanks, I'll try it. But I think REST is more elegant ✋.
The file refSeqs.json is generated by the API, so it depends on the Django server to be running. But I couldn't figure out yet why JBrowse can't load it.
Thank you for your reply. Machado is a very good Django framework. I plan to use it as part of my database. If the Jbrowse problem cannot be solved, I think I can try without using the REST framework.
You're welcome! I hope it's useful for you. Please, let us know whether the JBrowse configuration finally works for you and if have any problems.
Thanks, I'll try it. But I think REST is more elegant hand.
I think so too! The problem is that it takes too long to run a query in the database just the retrieve the chromosome sizes, while it happens almost immediately when you get it from the fasta file.
Also, if I want to treat the repetitive sequence as a feature value and make it searchable, just like genes, mRNA, and peptides. I added some test data to PostgreSQL, and added my cvterm to the MACHADO_VALID_TYPES variable in the settings.py , like this: MACHADO_VALID_TYPES = ['gene', 'mRNA', 'polypeptide', 'natural_transposable_element'] But when I rebuild the index through “python manage.py rebuild_index” , nothing seems to have changed. I think I used the wrong method, so I want to ask your opinion.
This is not configurable yet. Currently, the rebuild_index will index only the types set in this variable:
OVERLAPPING_FEATURES = ["SNV", "QTL", "copy_number_variation"]
Feel free to add a new type to this variable. You're welcome to contribute a PR moving this variable to the settings.py file.
Inactive for more than 10 days
Inactive for more than 10 days Sorry for not responding in time, because I took a long vacation before. I eventually plan to store the genome information in the data folder of Jbrowse.
That's all right. Please let us know about further development of your database and don't hesitate to contact us for assistance or suggestions.
Setup
Python version: Python 3.6.9 Operating system: CPython;Linux-4.15.0-142-generic-x86_64-with-Ubuntu-18.04-bionic
(Please copy and run the above in your Python, and copy-and-paste the output)
Expected behaviour
show the Jbrowse
Actual behaviour
I'm trying to establish a web project. But I encountered an unsolvable problem in jbrowse. I configure the trackList.json just like your document at https://machado.readthedocs.io/en/latest/jbrowse.html. But I got an error as shown in the picture above. My trackList.json is here:
{ "formatVersion" : 1, "refSeqs": "http://1.14.226.153:8000/api/jbrowse/refSeqs.json?soType=chromosome&organism=AAA%20aaa", "names" : { "type" : "REST", "url" : "http://1.14.226.153:8000/api/jbrowse/names", }, "tracks" : [ { "category": "1. Reference sequence", "useAsRefSeqStore": true, "label": "ref_seq", "key": "REST Reference Sequence", "type": "JBrowse/View/Track/Sequence", "storeClass": "JBrowse/Store/SeqFeature/REST", "baseUrl": "http://1.14.226.153:8000/api/jbrowse", "query": { "organism": "AAA aaa" } }, { "category": "2. Genes", "baseUrl" : "http://1.14.226.153:8000/api/jbrowse", "key" : "Gene", "label" : "gene", "query" : { "organism": "AAA aaa", "soType" : "gene" }, "storeClass" : "JBrowse/Store/SeqFeature/REST", "type" : "JBrowse/View/Track/CanvasFeatures", "style": { "label": "name,id", "description": "display" } }, { "category": "2. Genes", "baseUrl" : "http://1.14.226.153:8000/api/jbrowse", "key" : "Transcript", "label" : "transcripts", "query" : { "organism": "AAA aaa", "soType" : "mRNA" }, "storeClass" : "JBrowse/Store/SeqFeature/REST", "type" : "JBrowse/View/Track/CanvasFeatures", "style": { "label": "name,id", "description": "display" } }, { "category": "2. Genes", "baseUrl" : "http://1.14.226.153:8000/api/jbrowse", "key" : "CDS", "label" : "CDS", "query" : { "organism": "AAA aaa", "soType" : "CDS" }, "storeClass" : "JBrowse/Store/SeqFeature/REST", "type" : "JBrowse/View/Track/CanvasFeatures" } ] }
So I sincerely need your help!