Install/Upgrade Secret Management for Integration Modules
As of Clarity LIMS v5.4, the method used for managing passwords (secrets) for Clarity LIMS integration modules has changed.
Newer integration packages are not backward compatible with previous deployments that use file-based password storage.
Compatibility Overview
|
Module |
Prior Release |
Released with Clarity LIMS v5.4 and later |
Released with Clarity LIMS v6.2 and later |
Integration |
|---|---|---|---|---|
|
BaseSpaceLIMS-Pre-configured-Workflows-Package |
1.2.1.5 and 2.0 1.2.2 (released with NovaSeq v3.2.2, not supporting Vault / Secret Utility) |
2.1 |
Not applicable |
Not applicable |
|
BaseSpaceLIMS-Illumina-Preset-Protocols |
1.0.2 |
2.0 |
2.6.0 |
IPP |
|
Clarity LIMS-NGS-Package |
5.19 |
5.20 |
Not applicable |
NGS |
|
Clarity LIMS-NGS-Package-v5 |
Not applicable |
Not applicable |
5.23 |
NGS |
|
BaseSpaceLIMS-sequencer-api |
2.2.1.9 |
2.3 |
2.6.0 |
NovaSeq 6000/6000Dx API-based integration |
|
BaseSpaceLIMS-novaseq-sequencing-service |
2.2.2 |
2.3 |
2.5.0 |
NovaSeq 6000 file-based integration |
|
BaseSpaceLIMS-novaseq-extensions |
2.2.2 |
2.3 |
2.5.0 |
NovaSeq 6000 file-based integration |
|
HiSeq |
5.6.1 |
5.7 |
Not applicable |
HiSeq |
|
HiSeq 3k4k |
1.2.0.6 |
1.3 |
Not applicable |
HiSeq 3000/4000 |
|
HiSeq X |
1.5.0.5 |
1.6 |
Not applicable |
HiSeq X |
|
NextSeq 550 |
2.0.3 |
2.1 |
Not applicable |
NextSeq 550 |
|
ClarityLIMS-Illumina-NextSeq-Package-v2 |
Not applicable |
Not applicable |
2.3.0 |
NextSeq 550 |
|
MiSeq |
7.0 |
7.1 |
Not applicable |
MiSeq |
|
ClarityLIMS-Illumina-MiSeq-Package-v8 |
Not applicable |
Not applicable |
8.2.0 |
MiSeq |
|
MiSeq Dx |
1.7.0.5 |
1.8 |
Not applicable |
MiSeqDx |
|
BaseSpaceLIMS-miseqdx-sequencing-service |
Not applicable |
Not applicable |
1.10.0 |
MiSeqDx |
|
BaseSpaceLIMS-miseqdx-extensions |
Not applicable |
Not applicable |
1.10.0 |
MiSeqDx |
|
BaseSpaceLIMS-SIS-Core-Package |
Not applicable |
Not applicable |
2.4.0 |
NextSeq 1000/2000, iScan, NovaSeq X Series |
|
BaseSpaceLIMS-SIS-Nextseq1k2k-Package |
Not applicable |
Not applicable |
2.4.0 |
NextSeq 1000/2000 |
|
BaseSpaceLIMS-SIS-NovaSeqXSeries-Package |
Not applicable |
Not applicable |
1.1.0 |
NovaSeq X Series |
|
BaseSpaceLIMS-SIS-iScan-Package |
Not applicable |
Not applicable |
1.1.0 |
iScan |
|
BaseSpaceLIMS-unified-product-analytics |
Not applicable |
Not applicable |
1.2.0 |
Clarity LIMS Product Analytics |
|
BaseSpaceLIMS-unified-product-analytics-scripts |
Not applicable |
Not applicable |
1.2.0 |
Clarity LIMS Product Analytics |
Compatibility of Releases
| • | When installing Clarity LIMS v6.2 and later, only integration packages released with or after Clarity LIMS v6.2 are supported. |
| • | HiSeq, HiSeq 3k4k and HiSeq X are no longer supported from Clarity LIMS v6.0 and later. |
| • | When installing Clarity LIMS v5.4 and later, only integration packages released with or after Clarity LIMS v5.4 are supported. |
| • | A newer integration package can be installed on older Clarity LIMS releases (* existing individual package requirements still apply). In this scenario, there will be two password management processes in the system: |
| • | Existing file-based password storage: used by Clarity LIMS and any older integration packages. |
| • | New secret management (Secret Util RPM): used by the newer integration package. |
| • | Existing limitations or version compatibility of individual Integration packages with the Clarity LIMS version still apply. |
Installation Steps for Clarity LIMS v5.4 and Later
The following diagram shows the installation steps required for installing Secret Utility and integration packages with Clarity LIMS v5.4 and later.
| 1. | Install Clarity LIMS v6.0. |
| • | Install Clarity LIMS-App 6.0 and complete pending script. |
| • | Secret Utility (secretutil) is installed as part of Clarity LIMS-App 6.0 dependency, and the Secret Utility configuration is part of Clarity LIMS pending scripts. |
| 2. | Install Secret Utility. |
| • | In the automated installation tooling for Clarity LIMS v6.0, the installation and configuration of Secret Utility is included. No further action is necessary. |
| • | For manual installation: |
| a. | Install Clarity LIMS-SecretUtil. |
| b. | Configure Secret Utility by running the following script: /opt/gls/clarity/config/pending/05_configure_claritylims_secretutil.sh. |
Refer to Guide to Secret Management for details on configuring Secret Utility.
| 3. | Check usage of custom API username. |
| • | Check for any needs for custom API username, if any (eg novaseq_user). The documentation for the integration package provides the requirements for API username. |
In a typical installation, a default API username (apiuser) is used. It is not necessary to add the default apiuser username, because it is configured as part of Clarity LIMS v6.0 installation. If no custom API username is required, skip step 4 and proceed to step 5.
| 4. | Configure custom API username. |
| • | If a custom API username is not required, proceed to step 5. |
| • | If a custom API username is required, configure the user/password with Secret Utility as follows. Substitute the values enclosed in double quotes with your own values, keeping the double quotes. |
java -jar /opt/gls/clarity/tools/secretutil/secretutil.jar -n=INTEGRATION -u="password" "key"
Example:
java -jar /opt/gls/clarity/tools/secretutil/secretutil.jar -n=INTEGRATION -u="mypassword" "apiusers/novaseq_user"
| • | For a custom api username, set the key to apiusers/{custom api username} |
| 5. | Install integration package. |
There is no change to the installation of the integration package. Follow existing installation instructions.
The new configuration script in the new integration package retrieves passwords directly from Secret Utility.
For IAP access token and BSSH access token, follow the existing setup guide. There is no change in the configuration step.
