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feat: Allow Platform v24+ to communicate with a MySQL db NOTASK (#902)
* Allow Platform v24+ to communicate with a MySQL db * Add back the closing backtick Co-authored-by: Copilot <[email protected]> Signed-off-by: Alberto Chiusole <[email protected]> * Use equal sign in bash excerpt instead of colon sign Co-authored-by: Copilot <[email protected]> Signed-off-by: Alberto Chiusole <[email protected]> --------- Signed-off-by: Alberto Chiusole <[email protected]> Co-authored-by: Copilot <[email protected]>
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‎platform-enterprise_docs/enterprise/_templates/k8s/configmap.yml‎

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TOWER_SERVER_URL: "https://<YOUR PUBLIC TOWER HOST NAME>"
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TOWER_CONTACT_EMAIL: "[email protected]"
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TOWER_JWT_SECRET: "ReplaceThisWithALongSecretString"
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TOWER_DB_URL: "jdbc:mysql://<YOUR DB HOST NAME AND PORT>/tower"
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TOWER_DB_URL: "jdbc:mysql://<YOUR DB HOST NAME AND PORT>/tower?permitMysqlScheme=true"
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TOWER_DB_DRIVER: "org.mariadb.jdbc.Driver"
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TOWER_DB_USER: "tower"
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TOWER_DB_PASSWORD: "<YOUR DB PASSWORD>"

‎platform-enterprise_docs/enterprise/configuration/aws_parameter_store.md‎

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@@ -21,7 +21,7 @@ Due to the order of operations when deploying Seqera Enterprise, some configurat
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| ------------------------- | --------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------- |
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| `TOWER_DB_USER` | The user account to access your database. If you are using an external database, you must create this user manually. **For installation in a new environment, this value must be set as an environment variable.** | Default: `tower` |
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| `TOWER_DB_PASSWORD` | The user password to access your database. If you are using an external database, you must create this password manually. **For installation in a new environment, this value must be set as an environment variable.** | Default: `tower` |
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| `TOWER_DB_URL` | The URL to access your database. **For installation in a new environment, this value must be set as an environment variable.** | Example: `jdbc:mysql://db:3306/tower` |
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| `TOWER_DB_URL` | The URL to access your database. **For installation in a new environment, this value must be set as an environment variable.** | Example: `jdbc:mysql://db:3306/tower?permitMysqlScheme=true` |
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| `TOWER_APP_NAME` | Application name. To run multiple instances of the same Seqera account, each instance must have a unique name, e.g., `tower-dev` and `tower-prod`. **Can also be set in `tower.yml` with `tower.appName`.** | Default: `tower` |
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| `TOWER_ENABLE_AWS_SES` | Set `true` to enable AWS Simple Email Service for sending Seqera emails instead of SMTP. | Default: `false` |
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| `TOWER_ENABLE_PLATFORMS` | A comma-separated list of execution backends to enable. **At least one is required.** | `altair-platform,awsbatch-platform,awscloud-platform,azbatch-platform,eks-platform,googlebatch-platform,googlecloud-platform,gke-platform,k8s-platform,local-platform,lsf-platform,moab-platform,slurm-platform` |

‎platform-enterprise_docs/enterprise/configuration/configtables/db_aws.yml‎

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---
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AWS Parameter Store: '`{prefix}/datasources/default/username`'
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Description: >
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Description: >
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The user account to access your database.
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If you are using an external database, you must create this user manually. **For installation in a new environment, this value must be set as an environment variable.**
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Value: 'Default: `tower`'
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AWS Parameter Store: '`{prefix}/datasources/default/password`'
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Description: >
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Description: >
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The user password to access your database.
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If you are using an external database, you must create this password manually. **For installation in a new environment, this value must be set as an environment variable.**
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Value: 'Default: `tower`'
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AWS Parameter Store: '`{prefix}/datasources/default/url`'
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Description: >
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Description: >
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The URL to access your database. **For installation in a new environment, this value must be set as an environment variable.**
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Value: '`jdbc:mysql://db:3306/tower`'
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Value: '`jdbc:mysql://db:3306/tower?permitMysqlScheme=true`'
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AWS Parameter Store: '`{prefix}/datasources/default/minPoolSize`'
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Description: >
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Minimum database connection pool size.
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Description: >
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Minimum database connection pool size.
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Value: 'Default: `5`'
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AWS Parameter Store: '`{prefix}/datasources/default/maxPoolSize`'
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Description: >
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Maximum database connection pool size.
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Description: >
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Maximum database connection pool size.
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Value: 'Default: `10`'
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AWS Parameter Store: '`{prefix}/datasources/default/maxLifetime`'
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Description: >
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Maximum lifespan of database connections, in milliseconds.
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Description: >
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Maximum lifespan of database connections, in milliseconds.
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Value: 'Default: `1800000`'
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AWS Parameter Store: '`{prefix}/redisson/uri`'
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Description: >
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Description: >
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The URL to access your Seqera Redis instance.
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Value: 'Example: `redis://redis:6379`'
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AWS Parameter Store: '`{prefix}/redisson/password`'
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Description: >
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Description: >
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The password of your Seqera Redis instance.
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Value:
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Value:

‎platform-enterprise_docs/enterprise/configuration/configtables/db_env.yml‎

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---
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Environment variable: '`TOWER_DB_USER`'
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Description: >
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Description: >
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The user account to access your database.
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If you are using an external database, you must create this user manually.
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Value: 'Default: `tower`'
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Environment variable: '`TOWER_DB_PASSWORD`'
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Description: >
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Description: >
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The user password to access your database.
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If you are using an external database, you must create this password manually.
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Value: 'Default: `tower`'
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Environment variable: '`TOWER_DB_URL`'
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Description: >
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Description: >
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The URL to access your database.
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Value: 'Example: `jdbc:mysql://db:3306/tower`'
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Value: 'Example: `jdbc:mysql://db:3306/tower?permitMysqlScheme=true`'
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Environment variable: '`TOWER_DB_MIN_POOL_SIZE`'
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Description: >
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Minimum database connection pool size.
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Description: >
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Minimum database connection pool size.
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Value: 'Default: `5`'
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Environment variable: '`TOWER_DB_MAX_POOL_SIZE`'
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Description: >
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Maximum database connection pool size.
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Description: >
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Maximum database connection pool size.
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Value: 'Default: `10`'
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Environment variable: '`TOWER_DB_MAX_LIFETIME`'
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Description: >
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Maximum lifespan of database connections, in milliseconds.
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Description: >
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Maximum lifespan of database connections, in milliseconds.
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Value: 'Default: `1800000`'
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Environment variable: '`TOWER_REDIS_URL`'
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Description: >
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The URL to access your Seqera Redis instance.
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Description: >
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The URL to access your Seqera Redis instance.
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Value: 'Example: `redis://redis:6379`'
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Environment variable: '`TOWER_REDIS_PASSWORD`'
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Description: >
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Description: >
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The password of your Seqera Redis instance.
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Value:
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Value:

‎platform-enterprise_docs/enterprise/configuration/configtables/db_yml.yml‎

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---
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tower.yml: '`datasources.default.username`'
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Description: >
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Description: >
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The user account to access your database.
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If you are using an external database, you must create this user manually. **For installation in a new environment, this value must be set as an environment variable.**
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Value: 'Default: `tower`'
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tower.yml: '`datasources.default.password`'
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Description: >
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Description: >
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The user password to access your database.
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If you are using an external database, you must create this password manually. **For installation in a new environment, this value must be set as an environment variable.**
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Value: 'Default: `tower`'
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tower.yml: '`datasources.default.url`'
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Description: >
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Description: >
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The URL to access your database. **For installation in a new environment, this value must be set as an environment variable.**
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Value: 'Example: `jdbc:mysql://db:3306/tower`'
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Value: 'Example: `jdbc:mysql://db:3306/tower?permitMysqlScheme=true`'
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tower.yml: '`datasources.default.minPoolSize`'
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Description: >
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Minimum database connection pool size.
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Description: >
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Minimum database connection pool size.
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Value: 'Default: `5`'
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tower.yml: '`datasources.default.maxPoolSize`'
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Description: >
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Maximum database connection pool size.
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Description: >
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Maximum database connection pool size.
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Value: 'Default: `10`'
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tower.yml: '`datasources.default.maxLifetime`'
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Description: >
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Maximum lifespan of database connections, in milliseconds.
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Description: >
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Maximum lifespan of database connections, in milliseconds.
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Value: 'Default: `1800000`'
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tower.yml: '`redisson.uri`'
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Description: >
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Description: >
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The URL to access your Seqera Redis instance.
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Value: 'Example: `redis://redis:6379`'
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tower.yml: '`redisson.password`'
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Description: >
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Description: >
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The password of your Seqera Redis instance.
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Value:
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Value:

‎platform-enterprise_docs/enterprise/general_troubleshooting.md‎

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To resolve this issue for `Europe/Amsterdam` time zone, append `serverTimezone` to the value of [`TOWER_DB_URL`](./configuration/overview#seqera-and-redis-databases):
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```bash
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export TOWER_DB_URL": "jdbc:mysql://<YOUR_DATABASE_IP>:3306/tower?serverTimezone=Europe/Amsterdam"
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export TOWER_DB_URL="jdbc:mysql://<YOUR_DATABASE_IP>:3306/tower?permitMysqlScheme=true&serverTimezone=Europe/Amsterdam"
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```
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**_java.io.IOException: Unsupported protocol version 252_ error while completed or terminated runs display as in progress on Seqera**

‎platform-enterprise_versioned_docs/version-24.1/enterprise/_templates/k8s/configmap.yml‎

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Original file line numberDiff line numberDiff line change
@@ -8,7 +8,7 @@ data:
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TOWER_SERVER_URL: "https://<YOUR PUBLIC TOWER HOST NAME>"
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TOWER_CONTACT_EMAIL: "[email protected]"
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TOWER_JWT_SECRET: "ReplaceThisWithALongSecretString"
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TOWER_DB_URL: "jdbc:mysql://<YOUR DB HOST NAME AND PORT>/tower"
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TOWER_DB_URL: "jdbc:mysql://<YOUR DB HOST NAME AND PORT>/tower?permitMysqlScheme=true"
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TOWER_DB_DRIVER: "org.mariadb.jdbc.Driver"
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TOWER_DB_USER: "tower"
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TOWER_DB_PASSWORD: "<YOUR DB PASSWORD>"

‎platform-enterprise_versioned_docs/version-24.1/enterprise/configuration/aws_parameter_store.md‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -21,7 +21,7 @@ Due to the order of operations when deploying Seqera Enterprise, some configurat
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| ------------------------- | --------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------- |
2222
| `TOWER_DB_USER` | The user account to access your database. If you are using an external database, you must create this user manually. **For installation in a new environment, this value must be set as an environment variable.** | Default: `tower` |
2323
| `TOWER_DB_PASSWORD` | The user password to access your database. If you are using an external database, you must create this password manually. **For installation in a new environment, this value must be set as an environment variable.** | Default: `tower` |
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| `TOWER_DB_URL` | The URL to access your database. **For installation in a new environment, this value must be set as an environment variable.** | Example: `jdbc:mysql://db:3306/tower` |
24+
| `TOWER_DB_URL` | The URL to access your database. **For installation in a new environment, this value must be set as an environment variable.** | Example: `jdbc:mysql://db:3306/tower?permitMysqlScheme=true` |
2525
| `TOWER_APP_NAME` | Application name. To run multiple instances of the same Seqera account, each instance must have a unique name, e.g., `tower-dev` and `tower-prod`. **Can also be set in `tower.yml` with `tower.appName`.** | Default: `tower` |
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| `TOWER_ENABLE_AWS_SES` | Set `true` to enable AWS Simple Email Service for sending Seqera emails instead of SMTP. | Default: `false` |
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| `TOWER_ENABLE_PLATFORMS` | A comma-separated list of execution backends to enable. **At least one is required.** | `altair-platform,awsbatch-platform,azbatch-platform,eks-platform,googlebatch-platform,gke-platform,k8s-platform,local-platform,lsf-platform,moab-platform,slurm-platform` |

‎platform-enterprise_versioned_docs/version-24.1/enterprise/configuration/configtables/db_aws.yml‎

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---
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AWS Parameter Store: '`{prefix}/datasources/default/username`'
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Description: >
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Description: >
55
The user account to access your database.
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If you are using an external database, you must create this user manually. **For installation in a new environment, this value must be set as an environment variable.**
77
Value: 'Default: `tower`'
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-
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-
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AWS Parameter Store: '`{prefix}/datasources/default/password`'
10-
Description: >
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Description: >
1111
The user password to access your database.
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If you are using an external database, you must create this password manually. **For installation in a new environment, this value must be set as an environment variable.**
1313
Value: 'Default: `tower`'
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-
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AWS Parameter Store: '`{prefix}/datasources/default/url`'
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Description: >
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Description: >
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The URL to access your database. **For installation in a new environment, this value must be set as an environment variable.**
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Value: '`jdbc:mysql://db:3306/tower`'
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Value: '`jdbc:mysql://db:3306/tower?permitMysqlScheme=true`'
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AWS Parameter Store: '`{prefix}/datasources/default/minPoolSize`'
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Description: >
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Minimum database connection pool size.
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Description: >
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Minimum database connection pool size.
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Value: 'Default: `5`'
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-
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AWS Parameter Store: '`{prefix}/datasources/default/maxPoolSize`'
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Description: >
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Maximum database connection pool size.
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Description: >
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Maximum database connection pool size.
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Value: 'Default: `10`'
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AWS Parameter Store: '`{prefix}/datasources/default/maxLifetime`'
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Description: >
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Maximum lifespan of database connections, in milliseconds.
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Description: >
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Maximum lifespan of database connections, in milliseconds.
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Value: 'Default: `1800000`'
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-
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AWS Parameter Store: '`{prefix}/redisson/uri`'
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Description: >
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Description: >
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The URL to access your Seqera Redis instance.
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Value: 'Example: `redis://redis:6379`'
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AWS Parameter Store: '`{prefix}/redisson/password`'
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Description: >
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Description: >
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The password of your Seqera Redis instance.
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Value:
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Value:

‎platform-enterprise_versioned_docs/version-24.1/enterprise/configuration/configtables/db_env.yml‎

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Original file line numberDiff line numberDiff line change
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---
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Environment variable: '`TOWER_DB_USER`'
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Description: >
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Description: >
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The user account to access your database.
66
If you are using an external database, you must create this user manually.
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Value: 'Default: `tower`'
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-
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Environment variable: '`TOWER_DB_PASSWORD`'
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Description: >
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Description: >
1111
The user password to access your database.
1212
If you are using an external database, you must create this password manually.
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Value: 'Default: `tower`'
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-
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Environment variable: '`TOWER_DB_URL`'
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Description: >
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Description: >
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The URL to access your database.
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Value: 'Example: `jdbc:mysql://db:3306/tower`'
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Value: 'Example: `jdbc:mysql://db:3306/tower?permitMysqlScheme=true`'
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Environment variable: '`TOWER_DB_MIN_POOL_SIZE`'
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Description: >
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Minimum database connection pool size.
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Description: >
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Minimum database connection pool size.
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Value: 'Default: `5`'
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Environment variable: '`TOWER_DB_MAX_POOL_SIZE`'
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Description: >
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Maximum database connection pool size.
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Description: >
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Maximum database connection pool size.
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Value: 'Default: `10`'
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Environment variable: '`TOWER_DB_MAX_LIFETIME`'
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Description: >
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Maximum lifespan of database connections, in milliseconds.
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Description: >
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Maximum lifespan of database connections, in milliseconds.
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Value: 'Default: `1800000`'
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Environment variable: '`TOWER_REDIS_URL`'
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Description: >
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The URL to access your Seqera Redis instance.
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Description: >
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The URL to access your Seqera Redis instance.
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Value: 'Example: `redis://redis:6379`'
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Environment variable: '`TOWER_REDIS_PASSWORD`'
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Description: >
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Description: >
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The password of your Seqera Redis instance.
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Value:
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Value:

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