New Linux cBio setup

[Raktim Sinha]

Hi -

I am trying to setup cbio on a CentOS Linux release 7.9.2009 for the first time.

I ran into some trouble using `docker-compose up`, so trying to do it it step by step.

Ran: `docker-compose up cbioportal-database` 

How can I tell the Db has been provisioned correctly? I container is sitting at this prompt currently for a while now:

<..snip ..>

cbioportal-database-container  | 2024-07-29T20:08:22.070737Z 0 [Warning] 'user' entry 'root@localhost' ignored in --skip-name-resolve mode.
cbioportal-database-container  | 2024-07-29T20:08:22.070814Z 0 [Warning] 'user' entry 'mysql.session@localhost' ignored in --skip-name-resolve mode.
cbioportal-database-container  | 2024-07-29T20:08:22.070836Z 0 [Warning] 'user' entry 'mysql.sys@localhost' ignored in --skip-name-resolve mode.
cbioportal-database-container  | 2024-07-29T20:08:22.070910Z 0 [Warning] 'db' entry 'performance_schema mysql.session@localhost' ignored in --skip-name-resolve mode.
cbioportal-database-container  | 2024-07-29T20:08:22.070927Z 0 [Warning] 'db' entry 'sys mysql.sys@localhost' ignored in --skip-name-resolve mode.
cbioportal-database-container  | 2024-07-29T20:08:22.070974Z 0 [Warning] 'proxies_priv' entry '@ root@localhost' ignored in --skip-name-resolve mode.
cbioportal-database-container  | 2024-07-29T20:08:22.078372Z 0 [Warning] 'tables_priv' entry 'user mysql.session@localhost' ignored in --skip-name-resolve mode.
cbioportal-database-container  | 2024-07-29T20:08:22.078411Z 0 [Warning] 'tables_priv' entry 'sys_config mysql.sys@localhost' ignored in --skip-name-resolve mode.
cbioportal-database-container  | 2024-07-29T20:08:22.097260Z 0 [Note] Event Scheduler: Loaded 0 events
cbioportal-database-container  | 2024-07-29T20:08:22.097640Z 0 [Note] mysqld: ready for connections.
cbioportal-database-container  | Version: '5.7.22'  socket: '/var/run/mysqld/mysqld.sock'  port: 3306  MySQL Community Server (GPL)
cbioportal-database-container  | 2024-07-29T20:08:23.075860Z 0 [Note] InnoDB: Buffer pool(s) load completed at 240729 20:08:23

Many thanks!

-R

[de Bruijn, Ino]

Hi Raktim,

 

Did you run the init.sh scripts before? The database logs should indicate that they are loading the seed database

 

You can connect to the mysql database directly and check if you see any data inside of the database

 

Best wishes,

Ino

 

From: cbiop...@googlegroups.com <cbiop...@googlegroups.com> on behalf of Raktim Sinha <raktim...@gmail.com>
Date: Monday, July 29, 2024 at 5:33 PM
To: cBioPortal for Cancer Genomics Discussion Group <cbiop...@googlegroups.com>
Subject: [EXTERNAL] [cbioportal] New Linux cBio setup

Hi - I am trying to setup cbio on a CentOS Linux release 7. 9. 2009 for the first time. I ran into some trouble using `docker-compose up`, so trying to do it it step by step. Ran: `docker-compose up cbioportal-database`  How can I tell the Db

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