Opal plugins available are:
Opal search engine based on Elasticsearch 2.4. Can be used embedded in Opal (default)
or configured to connect to an Elasticsearch cluster.
|No dependencies||Search Plugin API|
Stores the genotypes in Variant Call Format (VCF) files (binary flavor, BCF, is also supported).
VCF/BCF files can be downloaded filtered by participant phenotype criteria.
|htslib executables (bcftools, tabix, bgzip)||VCF Store Plugin API|
|opal-datasource-limesurvey||opal-datasource||Connects to a Limesurvey database to extract variables and data.||No dependencies||Datasource Plugin API|
|opal-datasource-redcap||opal-datasource||Connects to a REDCap server to extract variables and data.||No dependencies||Datasource Plugin API|
|opal-datasource-spss||opal-datasource||Java implementation of a SPSS file reader.||No dependencies||Datasource Plugin API|
|opal-datasource-readr||opal-datasource||R implementation of a rectangular format file reader, based on readr.||R server||Datasource Plugin API|
|opal-datasource-readxl||opal-datasource||R implementation of a Excel file reader/writer, based on readxl/writexl.||R server||Datasource Plugin API|
|opal-datasource-googlesheets4||opal-datasource||R implementation of a Google Sheets reader, based on googlesheets4.||R server||Datasource Plugin API|
|opal-datasource-validate||opal-analysis||R implementation of a data and mete-data validator, based on validate.||R server||Analysis Plugin API|
All plugins are to be deployed as a directory at the following location: OPAL_HOME/plugins.
Because having a search engine is an absolute requirement, Opal server will check at startup that there is a plugin of type
opal-search and if it’s not the case, the latest version of the opal-search-es plugin (that applies to the current Opal server version) will be automatically downloaded and installed without needing a server restart. If for any reason this plugin cannot be automatically downloaded (network issue), the Opal start-up will fail and you will need to install the plugin manually.
Available plugins can be downloaded from OBiBa Plugins Repository. The manual installation procedure should be performed as follow:
- Download the plugin of interest (zip file) from OBiBa Plugins Repository,
- Unzip plugin package in OPAL_HOME/plugins folder. Note that the plugin folder name does not matter, Opal will discover the plugin through the plugin.properties file that is expected to be found in the plugin folder.
- Read the installation instructions (if any) of the plugin to identify the system dependencies or any other information,
- Restart Opal.
The OPAL_HOME/plugins folder contains all the Opal plugins that will be inspected at startup. A plugin is enabled if it has:
- A valid plugin.properties file,
- In case of several versions of the same plugin are installed, the latest one is selected.
The layout of the plugin folder is as follow:
OPAL_HOME/ └── plugins └── <plugin-folder> ├── lib │ └── <plugin-lib>.jar ├── LICENSE.txt ├── README.md ├── plugin.properties └── site.properties
Inside the plugin’s folder, a properties file, plugin.properties, has two sections:
- The required properties that describe the plugin (name, type, version etc.)
- Some default properties required at runtime (path to third-party executables for instance).
Still in the plugin’s folder, a site-specific properties file, site.properties, is to be used for defining the local configuration of the plugin. Note that this file will be copied when upgrading the plugin.
Opal assigns a data folder location to the plugin: OPAL_HOME/data/<plugin-name> where plugin-name is the name defined in the plugin.properties file. This folder is then the one to be backed-up.