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

[Garrett S. <ste...@gm...>]

Hi Charan,

To answer one of your questions first, you cannot have tracks without an
assembly. JBrowse needs the assembly to know what the
chromosomes/contigs/etc. are that the tracks are being displayed on.

As for your other questions, I'm not sure exactly what your setup is, so
I'll try to explain what I can. You mention an EC2 instance, but then the
screenshot you posted shows JBrowse being served locally. If you are
hosting JBrowse on an EC2 instance, you can't currently use the GUI editor
to add a local file. You'll have to do that with the CLI tool. Make sure
you are running the CLI tool on your EC2 instance, not your local machine.
You should probably run `jbrowse add-assembly` in the same directory you
ran `jbrowse create` in, which should be somewhere in your web server
(Apache, Nginx, etx.) directory (often that's "/var/www/html/", see this
guide <https://jbrowse.org/jb2/docs/superquickstart_web/> for a quick
example). Be aware that the command you posted will copy your .fa file into
your web server directory, since it needs to be publicly served by the web
server as well.

Let me know if that helps, or if I'm misunderstanding your setup.

Best,
Garrett

On Sun, Sep 19, 2021 at 1:56 AM Sunny Charan <cha...@gm...> wrote:

> 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
>