Re: [Gmod-ajax] JBrowse genome assemble setup issues

[Colin <col...@gm...>]

Hi there Charan!
I am sorry I missed this email awhile back. Were you able to resolve?


Generally, you use add-assembly command before add-track. The add-assembly
will create the config.json

Interested to see if there is a way to think about your S3 deployment. If
you wanted to use GUI admin server and an s3 bucket, I would develop it
locally, and then upload to S3 after you are finished

Note: Our JBrowse instance e.g. at https://jbrowse.org/code/jb2/v1.6.4 is
on an S3 bucket.

-Colin

On Mon, Sep 20, 2021 at 11:01 AM Charan Thoomu <
Cha...@eg...> wrote:

> Hi,
>
>
>
> 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:
>
>
>
> Approach 1: GUI
>
> 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?
>
>
>
>
>
>
>
>
>
> Approach 2: CLI
>
> 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 the '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.
>
>
>
> --
>
> Thanks,
>
> Charan
>
>
>
>
>
> Charan Thoomu
>
> Software Engineer
>
> eGenesis, Inc.
>
> 300 Technology Square, Suite 301
>
> Cambridge, MA 02139
>
> cha...@eg...
>
> www.egenesisbio.com
>
>
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