Re: [Gmod-ajax] Formats supported by JBrowse 2

[Sunny C. <cha...@gm...>]

Hi Garrett,

All our "fa, fai, gff3, gz, etc..." files are in the AWS S3 bucket and we
don't want to make our S3 bucket Public for security purposes.

I tried both GUI and CLI approaches for adding the files, I have doubts in
both the approaches as follows:

####GUI Approach####
While creating a new Genome Assembly, it is expecting only an URL , in our
case even if I give the S3 URL, it won't be able to fetch it because S3's
public access is blocked.

Is there an alternative way to create Genome Assembly without providing an
URL, instead adding from the EC2 instance is preferred?

[image: image.png]


####CLI Approach####

   1. Can I add tracks without adding assembly?
   2. I tried running " jbrowse add - track / data /*****.fa -- load copy"
   for adding tracks but I encountered -

"    Error: ENOENT: no such file or directory, open './config.json'
    Code: ENOENT
    Try this:
      * Make sure the file "./config.json" exists
      * Run `jbrowse add-assembly` to create a config file
"

   - If I have to run 'jbrowse add-assembly /data/*****.fa  --load copy'
   command, should I be in any specific directory to pick up the file? I am
   asking because when I run this command I am getting: " Error: Could not
   resolve to a file or a URL: " What am I missing here?

Please help me with detailed information.



On Mon, Aug 30, 2021 at 3:33 PM Garrett Stevens <ste...@gm...>
wrote:

> Hi Charan,
>
> I'm not sure I understand what you are describing. Where are these error
> messages you see? Screenshots could help. Also, can you describe how you
> are adding the tracks (e.g. via CLI add-track, or admin-server, etc.)?
>
> JBrowse does support tabix-indexed GFF3 files (e.g. myfile.gff3.gz with
> myfile.gff3.gz.tbi), so it seems like the files you want to use would be
> supported.
>
> Also, make sure the bucket serving the files has the correct CORS
> configuration (see here
> <https://github.com/GMOD/jbrowse-components/discussions/2216> for more
> details).
>
> Best,
> Garrett
>
> On Mon, Aug 30, 2021 at 12:22 PM Sunny Charan <cha...@gm...> wrote:
>
>> Hi,
>>
>> I am in the process of setting up JBrowse 2 (1.3.5) on AWS EC2 instance.
>>
>> So far I installed the JBrowse 2 but when I was trying to "Add Tracks"
>> using the Object URL from S3 bucket which are in the .gff3 and .gz
>> extension.  I see a prompt saying either one of the following:
>>
>>    1. Error: TypeError: NetworkError when attempting to fetch resources.
>>    2. This format is not supported by this version and is supported in
>>    the latest version. I am reiterating again that I am using the latest
>>    release 1.3.5.
>>
>> So, please help me further in doing the setup in a successful way where I
>> can upload the tracks without any issues. And also if there are any
>> specific file formats JBrowse 2 is supported which I am unaware of.
>>
>> --
>> Thanks,
>> Charan
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>

-- 
Thanks,
Charan