Assistance with setting up GBiC

[Steve Siecinski]

Hello GBiC team!

 

Our company recently acquired a GBiC license, and I’ve been trying to set up the server to fit our needs after its initial installation. I’ve been trying to use the documentation to figure out how to approach this, but I’ve hit a bit of a wall and I just want to make sure I’m not missing some other resource that I should be following.

 

Our goals are to

1. Host our GBiC on an AWS EC2 with an internally accessible link through Route 53 (this was set up by another team member and works well as far as I can tell).
2. Link the EC2-based GBiC to an EFS to store locally generated data that users can visualize on the genome browser, ideally organized by projects / hubs and somewhat automatable (as new files are added to the respective EFS directories, have those associated track hubs automatically add them).
3. Download commonly used public tracks to the EFS to avoid long load times due to ‘on the fly’ mode, but keep the online utility preserved for users want to load up additional web-based tracks for their specific needs.

 

The GBiC runs as expected in on-the-fly mode but I’m having difficulty getting our local data set up to display on it without the user having to submit custom tracks or hubs.

 

I’ve mounted the EFS to the EC2 and sym linked its gbdb and mysql folders to their respective locations to replace the locally generated folders and they seem to be working fine when, for example, I run `sudo bash browserSetup.sh -t main mirror hg19`. However, it’s not clear to me how I would set up this semi-automated system to host output files from our pipelines (ex. Bigwig, bigbed, hic, etc…) as they’re generated and added to the EFS.

 

I think I found a thread in the google group that is trying to do something similar to what I need but if there’s a more formal outline on how to accomplish it, I’d really appreciate being pointed to it!

 

Thanks for putting together this great tool and I look forward to hearing from you.

Best,

-Steve

 

Stephen Siecinski

Scientist, Computational Biology

Omega Therapeutics

20 Acorn Park Drive, Suite 400

Cambridge, MA 02140

(908) 319-5006 (Mobile)

ssiec...@omegatx.com

 

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[Jairo Navarro Gonzalez]

Hello,

Thank you for using the UCSC Genome Browser and sending your inquiry.

There may be a simple solution that involves setting a "default cart" to enable custom viewing options such as changing the default assembly or attaching hubs automatically. You can learn more about customizing the default cart on the following help page, https://genome.ucsc.edu/goldenpath/help/gbib.html#Defaults. Using the default cart feature, you will be able to create a hub with all of the locally generated data and add any new data through the trackDb.txt file. This hub will then be automatically connected to any user accessing your mirror, even after they reset all the user settings.

I hope this is helpful. If you have any further questions, please reply to genome...@soe.ucsc.edu.
All messages sent to that address are archived on a publicly accessible Google Groups forum.
If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Jairo Navarro
UCSC Genome Browser

Want to share the Browser with colleagues?
Host a workshop: https://bit.ly/ucscTraining

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[Steve Siecinski]

Hell Jairo,

 

When I try following the instructions in the link that you provided, I encounter the following error when trying to create a new account for our internally hosted server.

 

“Can't start query:

INSERT INTO gbMembers SET userName='(redacted)',realName='(redacted)',password='(redacted)',email='(redacted)@ (redacted),lastUse=NOW(),accountActivated='Y'

mySQL error 1364: Field 'newPassword' doesn't have a default value (profile=<noProfile>, host=localhost, db=hgcentral)

 

Part of the issue might be that we’re using UCSC browser in the cloud, while the tutorial is for UCSC browser in a box. Is there a similar tutorial for creating the default configuration for the UCSC BIC version of the server? I’m guessing there might be additional configuration steps that are required to enable user accounts and access to locally hosted tracks.

 

Following up on the details of the AWS instance we’re using, I created a clean instance (tx3.large) running Ubuntu Server 20.04 LTS (HVM), SSD Volume Type and running the browserSetup.sh script provided by

https://genome-store.ucsc.edu/media/products/browserSetup.sh

 

Any additional assistance you could provide would really be appreciated. The

 

Best,

-Steve

 

From: Jairo Navarro Gonzalez <jnav...@ucsc.edu>
Date: Monday, January 24, 2022 at 9:00 AM
To: Steve Siecinski <ssiec...@omegatx.com>
Cc: genome...@soe.ucsc.edu <genome...@soe.ucsc.edu>
Subject: Re: [genome-mirror] Assistance with setting up GBiC

EXTERNAL EMAIL: Use caution with links and attachments.

[Brian Lee]

Dear Steve,

Thank you for using the UCSC Genome Browser and informing us of this experience.

We believe the issue is that a warning by the MySQL operations that is permissible in our other software instances, is not being allowed in your instance. If this is the cause, a temporary work-around for your installation could be to set sql-mode="" manually for your mysql/mariadb server.cnf installation, that is to set the sql-mode="" in /etc/my.cnf for your GBiC.

Thank you again for your inquiry and for using the UCSC Genome Browser. If you have any further public questions, please send new questions to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly accessible forum to help others find answers to similar questions. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu, which is a private internal list to our support team.

All the best,

To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/DM6PR17MB317850E7C0F8732FA2589238C1349%40DM6PR17MB3178.namprd17.prod.outlook.com.

[Steve Siecinski]

Hi Brian,

 

Thanks for the quick response. I do not have an /etc/my.cnf file after running sudo bash browserSetup.sh install but there is one in /etc/mysql/my.cnf, which is included below. I also noticed an issue when I try to run

 

sudo bash browserSetup.sh -b mysql

 

ERROR 1396 (HY000) at line 1: Operation CREATE USER failed for 'readonly'@'localhost'

Exit error 1 occurred on line 1

 

I’ve included the complete debugging log (reran the function with the -x flag) as an attachment. I hope this helps narrow the range of potential issues but please let me know if there are other troubleshooting steps I could take.

 

Best,

-Steve

 

# The MariaDB configuration file

#

# The MariaDB/MySQL tools read configuration files in the following order:

# 1. "/etc/mysql/mariadb.cnf" (this file) to set global defaults,

# 2. "/etc/mysql/conf.d/*.cnf" to set global options.

# 3. "/etc/mysql/mariadb.conf.d/*.cnf" to set MariaDB-only options.

# 4. "~/.my.cnf" to set user-specific options.

#

# If the same option is defined multiple times, the last one will apply.

#

# One can use all long options that the program supports.

# Run program with --help to get a list of available options and with

# --print-defaults to see which it would actually understand and use.

 

#

# This group is read both both by the client and the server

# use it for options that affect everything

#

[client-server]

 

# Import all .cnf files from configuration directory

!includedir /etc/mysql/conf.d/

!includedir /etc/mysql/mariadb.conf.d/

[mysqld]

default-authentication-plugin=mysql_native_password

[Matthew Speir]

Hi, Steve. 

I apologize for the delay in our reply. We're still debugging the issue with the browserSetup.sh script. We hope to have it resolved soon and will let you know when we have a new version available for you to try out. 

Thank you for your patience. 

---

Matthew Speir

UCSC Cell Browser, Quality Assurance and Data Wrangler

Human Cell Atlas, User Experience Researcher

UCSC Genome Browser, User Support

UC Santa Cruz Genomics Institute

Revealing life’s code.

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[Steve Siecinski]

Thanks for the update Matthew, we’re excited to get our server up and running and appreciate the support