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Last pushed: 2 years ago
Short Description
A demo GA4GH reference server
Full Description

This is a Docker image of a GA4GH reference server.

This was created by following the GA4GH reference implementation installation instructions.

Quickstart

$ docker pull abeconnelly/ga4gh-server
$ docker run -p 8185:80 abeconnelly/ga4gh-server
$ firefox localhost:8185/ga4gh

Basic Functionality

The following command can be issued from the command line after the ga4gh-server Docker image has started (outside of the running docker container). These commands are meant to be illustrative and don't necessarily issue meaningful requests.

# http://ga4gh.org/documentation/api/v0.5.1/ga4gh_api.html#/schema/org.ga4gh.GASearchCallSetsRequest
curl --data '{"variantSetIds":["1kg-phase1"], "name":null}' \
  --header 'Content-Type: application/json' \
  http://localhost:8185/ga4gh/v0.5.1/callsets/search | jq .

# http://ga4gh.org/documentation/api/v0.5.1/ga4gh_api.html#/schema/org.ga4gh.GASearchReadGroupSetsRequest
curl --data '{"datasetIds":[], "name":null}' \
  --header 'Content-Type: application/json' \
  http://localhost:8185/ga4gh/v0.5.1/readgroupsets/search | jq .


# http://ga4gh.org/documentation/api/v0.5.1/ga4gh_api.html#/schema/org.ga4gh.GASearchReadsRequest
curl --data '{"readGroupIds":["low-coverage:HG00533.mapped.ILLUMINA.bwa.CHS.low_coverage.20120522"], "referenceNname":null, "referenceId":null, "start":0}' \
  --header 'Content-Type: application/json' \
  http://localhost:8185/ga4gh/v0.5.1/reads/search | jq .

# http://ga4gh.org/documentation/api/v0.5.1/ga4gh_api.html#/schema/org.ga4gh.GASearchReferenceSetsRequest
curl --data '{"md5checksums":[], "accessions":[], "assemblyById":null }'  \
  --header 'Content-Type: application/json'  \
  http://localhost:8185/ga4gh/v0.5.1/referencesets/search | jq .


# http://ga4gh.org/documentation/api/v0.5.1/ga4gh_api.html#/schema/org.ga4gh.GASearchVariantsRequest
curl --data '{"variantSetIds":["1kg-phase1"], "callSetIds":[], "referenceName":"???", "start":1, "end":10000}'  \
  --header 'Content-Type: application/json'  \
  http://localhost:8185/ga4gh/v0.5.1/variants/search | jq .


# http://ga4gh.org/documentation/api/v0.5.1/ga4gh_api.html#/schema/org.ga4gh.GASearchVariantSetsRequest
curl --data '{"datasetIds":[]}' \
  --header 'Content-Type: application/json' \
  http://localhost:8185/ga4gh/v0.5.1/variantsets/search | jq .
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abeconnelly

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