[Gmod-ajax] JBrowse genome assemble setup issues

[Charan T. <Cha...@eg...>]

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...<mailto:cha...@eg...>
www.egenesisbio.com<http://www.egenesisbio.com/>