Questions on local installation of EDGE

[Amy Xiao]

Hi EDGE team,

I am currently trying a direct installation of EDGE in my HPC environment, as the HPC help team prefers direct installation as opposed to containerized installation. I am following the instructions here: https://edge.readthedocs.io/en/latest/installation.html#edge-configuration-1

If I only want to use the command line interface, can you advise whether I can stop after 4.1/4.1.1 and skip all other steps (4.1.2 - 4.1.6)? It's unclear to me if the user management system is a requirement, and I don't have permission to use sudo on my system.

Thanks for your advice!

Best,

Amy

[Lo, Chien-Chi]

Hi Amy,

 

Thank you for choosing EDGE for your needs.

 

For your purposes on command line interface only usage, you can proceed up to version 4.1.1. However, please note that version 4.1.5 is an exception, as it is essential for the proper functioning of the "Specialty Genes Profiling" module.

 

To better assist you, could you please specify which function or module of EDGE you are interested in using? Feel free to reach out to us with any questions or clarifications regarding EDGE – we're here to help.

 

Looking forward to hearing from you.

 

Best regards,

Chienchi

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[Amy Xiao]

Hi Chienchi,

Thanks for your advice, and I apologize for the delayed response.

For command line only usage, I will proceed with step 4.1.1. Can you confirm whether I still need to do step 4.1.6 (configure EDGE)?

I am interested in using EDGE for pre-processing, assembly/annotation, taxonomic classification, and ideally virulence gene identification (which would require step 4.1.5). I see in the installation instructions that step 4.1.5 requires me to run mysql to grant privileges to 'yourDBUsername'@'localhost'. Does this mean that if I want to do virulence gene identification, I will have to go through steps 4.1.3, 4.1.4, and 4.1.5?

Thanks for your help!

Best,

Amy

[Lo, Chien-Chi]

Hi Amy,

 

No problem at all. For the 4.1.5, you do need Mysql installed and someone with mysql root permission to help you create an db user for you and perform the 4.1.5 step 2 for you.  

 

## cmd to to create a db user.

mysql> CREATE USER 'yourDBUsername'@'localhost' IDENTIFIED BY 'yourDBPassword';

The section 4.1.3, 4.1.4 and 4.1.6 focus on user management system and front end GUI which the command line only usage is not required.  

 

Hope this clear on your question a bit.

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