htsget-refserver

README

htsget Reference Server

Reference server implementation of the htsget API protocol for securely streaming genomic data. For more information about htsget, see the paper or specification.

A GA4GH-hosted instance of this server is running at https://htsget.ga4gh.org/. To use, see the OpenAPI documentation.

Quickstart - Docker

We suggest running the reference server as a docker container, as the image comes pre-installed with all dependencies.

With docker installed, run:

docker image pull ga4gh/htsget-refserver:${TAG}

to pull the image, and:

docker container run -d -p 3000:3000 ga4gh/htsget-refserver:${TAG}

to spin up a containerized server. Custom config files can also be passed to the application by first mounting the directory containing the config, and specifying the path to config in the run command:

docker container run -d -p ${PORT}:${PORT} -v /directory/to/config:/usr/src/app/config ga4gh/htsget-refserver:${TAG} ./htsget-refserver -config /usr/src/app/config/config.json

Additional BAM/CRAM/VCF/BCF directories you wish to serve via htsget can also be mounted into the container. See the Configuration section below for instructions on how to serve custom datasets.

The full list of tags/versions is available on the dockerhub repository page.

Setup - Native

To run and/or develop the server natively on your OS, the following dependencies are required:

• Golang and language tools (tested on version 1.13)
• samtools (tested on version 1.9)
• bcftools (tested on version 1.10.2)
• htsget-refserver-utils (1.0.0+)

This project uses Go modules to manage packages and dependencies.

With the above dependencies installed, run:

git clone https://github.com/ga4gh/htsget-refserver.git
cd htsget-refserver

to clone and enter the repository, and:

go build -o ./htsget-refserver ./cmd

to build the application binary. To start, run:

./htsget-refserver

A custom config file can also be specified with -config:

./htsget-refserver -config /path/to/config.json

Configuration

The htsget web service can be configured with runtime parameters via a JSON config file, specified with -config. For example:

./htsget-refserver -config /path/to/config.json

Examples of valid JSON config files are available in this repository:

• ga4gh instance config - used to run the GA4GH-hosted instance at https://htsget.ga4gh.org
• local development config - used to run the local instance for development
• integration tests config - used for integration testing on Travis CI builds
• example 0 config
• empty config

In the JSON file, the root object must have a single "htsgetConfig" property, containing all sub-properties. ie:

{
    "htsgetConfig": {}
}

Configuration - "props" object

Under the htsgetConfig property, the props object overrides application-wide settings. The following table indicates the attributes of props and what settings they affect.

Name	Description	Default Value
port	the port on which the service will run	3000
host	web service hostname. The JSON ticket returned by the server will reference other endpoints, using this hostname/base url to provide a complete url.	http://localhost:3000/
docsDir	path to static file directory containing server documentation (e.g. OpenAPI). the server will serve its contents at the /docs/ endpoint	NONE
tempDir	writes temporary files used in request processing to this directory	.
logFile	writes application logs to this file	htsget-refserver.log
corsAllowedOrigins	CORS allow client from origins. Use comma to separate for multiple origins.	http://localhost
corsAllowedMethods	CORS allow methods.	GET, POST, PUT, DELETE, OPTIONS
corsAllowedHeaders	CORS allow headers.	*
corsAllowCredentials	CORS allow credentials.	false
corsMaxAge	CORS max age in seconds.	300
awsAssumeRole	Turn on awsAssumeRole middleware. See Private Bucket section below.	false

Example props object:

{
    "htsget": {
        "props": {
            "port": "80",
            "host": "https://htsget.ga4gh.org/",
            "tempdir": "/tmp/",
            "logfile": "/usr/src/app/htsget-refserver.log",
            "corsAllowedOrigins": "https://portal.ga4gh.org, http://intranet.ga4gh.org",
        }
    }
}

Configuration - "reads" object

Under the htsgetConfig property, the reads object overrides settings for reads-related data and endpoints. The following properties can be set:

• enabled (boolean): if true, the server will set up reads-related routes (ie. /reads/{id}, /reads/service-info). True by default.
• dataSourceRegistry (object): allows the server to serve alignment data from multiple cloud or local storage sources by mapping request object id patterns to registered data sources. A single sources property contains an array of data sources. For each data source, the following properties are required:
  • pattern - a regex pattern that the id in /reads/{id} is matched against. If an id matches the pattern, the server will attempt to load data from the specified source. The pattern should make use of named capture group(s) to populate the path to the file.
  • path - the path template (either by url or local file path) to alignment files matching the pattern. The path must indicate how named capture groups in the pattern will populate the path to the file.
• serviceInfo (object): specify the attribute values returned in the Service Info response from /reads/service-info. Default attributes are supplied if not provided by config. Allows modification of the following properties from the Service Info specification:
  • id
  • name
  • description
  • organization
  • contactUrl
  • documentationUrl
  • createdAt
  • updatedAt
  • environment
  • version)

Example reads object:

{
    "htsgetConfig": {
        "reads": {
            "enabled": true,
            "dataSourceRegistry": {
                "sources": [
                    {
                        "pattern": "^tabulamuris\\.(?P<accession>10X.*)$",
                        "path": "https://s3.amazonaws.com/czbiohub-tabula-muris/10x_bam_files/{accession}_possorted_genome.bam"
                    },
                    {
                        "pattern": "^tabulamuris\\.(?P<accession>.*)$",
                        "path": "https://s3.amazonaws.com/czbiohub-tabula-muris/facs_bam_files/{accession}.mus.Aligned.out.sorted.bam"
                    }
                ]
            }
            "serviceInfo": {
                "id": "demo.reads",
                "name": "htsget demo reads",
                "description": "serve alignment data via htsget",
                "organization": {
                    "name": "Example Org",
                    "url": "https://exampleorg.com"
                },
                "contactUrl": "mailto:nobody@exampleorg.com",
                "documentationUrl": "https://htsget.exampleorg.com/docs",
                "createdAt": "2021-01-01T09:00:00Z",
                "updatedAt": "2021-01-01T09:00:00Z",
                "environment": "test",
                "version": "1.0.0"
            }
        }
    }
}

Configuration - "variants" object

Under the htsgetConfig property, the variants object overrides settings for variants-related data and endpoints. The following properties can be set:

• enabled (boolean): if true, the server will set up variants-related routes (ie. /variants/{id}, /variants/service-info). True by default.
• dataSourceRegistry (object): allows the server to serve variant data from multiple cloud or local storage sources by mapping request object id patterns to registered data sources. A single sources property contains an array of data sources. For each data source, the following properties are required:
  • pattern - a regex pattern that the id in /variants/{id} is matched against. If an id matches the pattern, the server will attempt to load data from the specified source. The pattern should make use of named capture group(s) to populate the path to the file.
  • path - the path template (either by url or local file path) to variant files matching the pattern. The path must indicate how named capture groups in the pattern will populate the path to the file.
• serviceInfo (object): specify the attribute values returned in the Service Info response from /variants/service-info. Default attributes are supplied if not provided by config. Allows modification of the following properties from the Service Info specification:
  • id
  • name
  • description
  • organization
  • contactUrl
  • documentationUrl
  • createdAt
  • updatedAt
  • environment
  • version)

Example variants object:

{
    "htsgetConfig": {
        "variants": {
            "enabled": true,
            "dataSourceRegistry": {
                "sources": [
                    {
                        "pattern": "^1000genomes\\.(?P<accession>.*)$",
                        "path": "https://ftp-trace.ncbi.nih.gov/1000genomes/ftp/phase1/analysis_results/integrated_call_sets/{accession}.vcf.gz"
                    }
                ]
            }
            "serviceInfo": {
                "id": "demo.variants",
                "name": "htsget demo variants",
                "description": "serve variant data via htsget",
                "organization": {
                    "name": "Example Org",
                    "url": "https://exampleorg.com"
                },
                "contactUrl": "mailto:nobody@exampleorg.com",
                "documentationUrl": "https://htsget.exampleorg.com/docs",
                "createdAt": "2021-01-01T09:00:00Z",
                "updatedAt": "2021-01-01T09:00:00Z",
                "environment": "test",
                "version": "1.0.0"
            }
        }
    }
}

Private Bucket

• Turn on awsAssumeRole middleware request interceptor to support AWS Assume Role temporary security credentials loading to access S3 private bucket.

• When it is not configured, the default awsAssumeRole set to false such that execution environment know how to access S3 private bucket through AWS standard mechanism. In that case, see htslib AWS S3 plugin for credentials loading requirement.

Say, you have data in private bucket as follows:

s3://my-primary-data-prod/Project/PID00115/WGS/PID00115-final.bam

Example configuration:

{
  "htsgetConfig": {
    "props": {
      ...
      "awsAssumeRole": true
    },
    "reads": {
      ...
      "dataSourceRegistry": {
        "sources": [
          ...
          {
            "pattern": "^my-primary-data(?P<accession>.*)$",
            "path": "s3://my-primary-data{accession}"
          }
        ]
      },
      "serviceInfo": {
        ...
      }
    },
    "variants": {
      ...
      "dataSourceRegistry": {
        "sources": [
          ...
          {
            "pattern": "^my-primary-data(?P<accession>.*)$",
            "path": "s3://my-primary-data{accession}"
          }
        ]
      },
      "serviceInfo": {
        ...
      }
    }
  }
}

Then you can call Htsget as follows:

curl -s http://localhost:3000/reads/my-primary-data-prod/Project/PID00115/WGS/PID00115-final.bam | jq

Testing

To execute unit and end-to-end tests on the entire package, run:

go test ./... -coverprofile=cp.out

The go coverage report will be available at ./cp.out. To execute tests for a specific package (for example the htsrequest package) run:

go test ./internal/htsrequest -coverprofile=cp.out

Changelog

v1.5.0

• Supports configurable CORS headers

v1.4.0

• Server supports experimental POST method for endpoint /reads/{id}. Multiple genomic regions can be requested in a single request. See hts-specs PR #285 for more info.

v1.3.0

• Server supports reads and/or variants service-info endpoints. The attributes of the service-info response can be specified via the config file independently for each datatype

v1.2.0

• Server supports htsget /variants/{id} endpoint, streams VCFs via htsget protocol using bcftools dependency

v1.1.0

• Added support for configurable data sources via a data source registry specified in config file
• server can stream reads data via htsget protocol from any url or local file specified via config

v1.0.0

• Initial release

Roadmap

• Implement POST request functionality

Maintainers

• Jeremy Adams (jb-adams) jeremy.adams@ga4gh.org
• David Liu (xngln)

Issues

Bugs and issues can be submitted via the Github Issue Tracker