# User Manual - [Installation](https://docs.opencga.opencb.org/develop-2/manual/installation.md) - [Kubernetes Cluster](https://docs.opencga.opencb.org/develop-2/manual/installation/kubernetes.md) - [Azure](https://docs.opencga.opencb.org/develop-2/manual/installation/kubernetes/azure.md) - [Configuration](https://docs.opencga.opencb.org/develop-2/manual/installation/kubernetes/configuration.md) - [On-Premise HPC Cluster](https://docs.opencga.opencb.org/develop-2/manual/installation/compute-cluster.md) - [Server Configuration](https://docs.opencga.opencb.org/develop-2/manual/installation/compute-cluster/server-configuration.md) - [Getting OpenCGA](https://docs.opencga.opencb.org/develop-2/manual/installation/compute-cluster/building-from-source.md) - [Choosing Variant Storage Engine](https://docs.opencga.opencb.org/develop-2/manual/installation/compute-cluster/chosing-variant-storage.md): HBase vs. MongoDB - [Configuration](https://docs.opencga.opencb.org/develop-2/manual/installation/compute-cluster/configuration.md) - [Running Docker](https://docs.opencga.opencb.org/develop-2/manual/installation/docker.md) - [Login](https://docs.opencga.opencb.org/develop-2/manual/login.md) - [Using OpenCGA](https://docs.opencga.opencb.org/develop-2/manual/using-opencga.md): You can interact with your data in OpenCGA in several different ways, find the one that suits you most and get started! - [REST Web Service API](https://docs.opencga.opencb.org/develop-2/manual/using-opencga/restful-web-service-api.md): Understanding REST web service API - [IVA Web App](https://docs.opencga.opencb.org/develop-2/manual/using-opencga/iva-web-app.md): A rich web app front-end to work with OpenCGA - [Client Libraries](https://docs.opencga.opencb.org/develop-2/manual/using-opencga/client-libraries.md): Java, Python, R and Javascript clients are implemented - [pyopencga - Python Library](https://docs.opencga.opencb.org/develop-2/manual/using-opencga/client-libraries/python.md): If you're a Python user and you're keen of running OpenCGA through Python, you're in the right place! - [opencgaR - R library](https://docs.opencga.opencb.org/develop-2/manual/using-opencga/client-libraries/r.md): If you're a R user and you're keen of running OpenCGA through R, you're in the right place! - [Java](https://docs.opencga.opencb.org/develop-2/manual/using-opencga/client-libraries/java.md) - [JavaScript](https://docs.opencga.opencb.org/develop-2/manual/using-opencga/client-libraries/javascript.md) - [Command Line](https://docs.opencga.opencb.org/develop-2/manual/using-opencga/command-line.md) - [Configuration](https://docs.opencga.opencb.org/develop-2/manual/using-opencga/command-line/configuration.md) - [Files](https://docs.opencga.opencb.org/develop-2/manual/using-opencga/command-line/files.md): opencga.sh files - [Public Demo](https://docs.opencga.opencb.org/develop-2/manual/using-opencga/public-demo.md) - [Managing Data](https://docs.opencga.opencb.org/develop-2/manual/data-management.md) - [Working with Projects and Studies](https://docs.opencga.opencb.org/develop-2/manual/data-management/projects-and-studies.md) - [Loading of VCF files](https://docs.opencga.opencb.org/develop-2/manual/data-management/ingestion-of-vcf-files.md): This page describes the process that an operator follows to load their VCF files into an OpenCGA Variant Store. - [Working with Files](https://docs.opencga.opencb.org/develop-2/manual/data-management/working-with-files.md) - [Sharing and Permissions](https://docs.opencga.opencb.org/develop-2/manual/data-management/sharing-and-permissions.md) - [Users and Groups](https://docs.opencga.opencb.org/develop-2/manual/data-management/sharing-and-permissions/users-and-groups.md) - [Study ACLs](https://docs.opencga.opencb.org/develop-2/manual/data-management/sharing-and-permissions/permissions.md) - [Population of metadata](https://docs.opencga.opencb.org/develop-2/manual/data-management/population-of-metadata.md) - [Data Versioning](https://docs.opencga.opencb.org/develop-2/manual/data-management/population-of-metadata/data-versioning.md) - [Adding Custom Metadata](https://docs.opencga.opencb.org/develop-2/manual/data-management/population-of-metadata/adding-custom-metadata.md) - [Alignment Engine](https://docs.opencga.opencb.org/develop-2/manual/alignment-engine.md) - [BAM Index](https://docs.opencga.opencb.org/develop-2/manual/alignment-engine/bam-index.md) - [Alignment Read Query](https://docs.opencga.opencb.org/develop-2/manual/alignment-engine/alignment-read-query.md) - [Working with Coverage](https://docs.opencga.opencb.org/develop-2/manual/alignment-engine/working-with-coverage.md) - [Alignment Analysis](https://docs.opencga.opencb.org/develop-2/manual/alignment-engine/alignment-analysis.md) - [Variant Storage Engine](https://docs.opencga.opencb.org/develop-2/manual/variant-storage-engine.md) - [Variant Query](https://docs.opencga.opencb.org/develop-2/manual/variant-storage-engine/variant-query.md) - [Variant Aggregation Stats](https://docs.opencga.opencb.org/develop-2/manual/variant-storage-engine/variant-aggregation-stats.md) - [Variant Analysis](https://docs.opencga.opencb.org/develop-2/manual/variant-storage-engine/variant-analysis.md) - [Clinical Genomics](https://docs.opencga.opencb.org/develop-2/manual/clinical-genomics.md) - [Clinical Interpretation](https://docs.opencga.opencb.org/develop-2/manual/clinical-genomics/clinical-interpretation.md) - [Clinical Analysis](https://docs.opencga.opencb.org/develop-2/manual/clinical-genomics/clinical-analysis.md) - [Using JupyterLab](https://docs.opencga.opencb.org/develop-2/manual/using-jupyterlab.md) - [Administrator](https://docs.opencga.opencb.org/develop-2/manual/administrator.md) - [User Management](https://docs.opencga.opencb.org/develop-2/manual/administrator/user-management.md) - [Templates / Manifest](https://docs.opencga.opencb.org/develop-2/manual/administrator/templates-manifest.md) --- # Agent Instructions: Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter: ``` GET https://docs.opencga.opencb.org/develop-2/manual.md?ask= ``` The question should be specific, self-contained, and written in natural language. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.