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Routines for ingesting metadata to a CanDIG repository

Project description

Routines for ingesting metadata into a CanDIG 1.0 server Requires [candig-server](, [docopt]( and [pandas](

  • Free software: GNU General Public License v3

You can run the ingestion and test a server with the resulting repo as follows (requires Python 2.7 for the candig server)

# Install
virtualenv test_server
cd test_server
source bin/activate
pip install --upgrade pip setuptools
pip install git+
pip install git+
pip install git+
pip install git+

# setup initial peers
mkdir -p ga4gh/server/templates
touch ga4gh/server/templates/initial_peers.txt

# ingest data and make the repo
mkdir ga4gh-example-data
ingest ga4gh-example-data/registry.db <path to example data, like: mock_data/clinical_metadata_tier1.json>

# optional
# add peer site addresses
candig_repo add-peer ga4gh-example-data/registry.db <peer site IP address, like:>

# optional
# create dataset for reads and variants
candig_repo add-dataset --description "Reads and variants dataset" ga4gh-example-data/registry.db read_and_variats_dataset

# optinal
# add reference set, data source: or
candig_repo add-referenceset ga4gh-example-data/registry.db <path to downloaded reference set, like GRCh37-lite.fa> -d "GRCh37-lite human reference genome" --name GRCh37-lite --sourceUri ""

# optional
# add reads
candig_repo add-readgroupset -r -I <path to bam index file> -R GRCh37-lite ga4gh-example-data/registry.db read_and_variats_dataset <path to bam file>

# optional
# add variants
candig_repo add-variantset -I <path to variants index file> -R GRCh37-lite ga4gh-example-data/registry.db read_and_variats_dataset <path to vcf file>

# optional
# add sequence ontology set
# wget
candig_repo add-ontology ga4gh-example-data/registry.db <path to sequence ontology set, like: so.obo> -n so-xp

# optional
# add features/annotations
## get the following scripts
## download the relevant annotation release from Gencode
## decompress
# gunzip gencode.v27.annotation.gff3.gz
## buid the annotation database
# python -i gencode.v27.annotation.gff3 -o gencode.v27.annotation.db -v
# add featureset
candig_repo add-featureset ga4gh-example-data/registry.db read_and_variats_dataset <path to the annotation.db> -R GRCh37-lite -O so-xp

# optional
# add phenotype association set from Monarch Initiative
# wget
candig_repo add-phenotypeassociationset ga4gh-example-data/registry.db read_and_variats_dataset <path to the folder containing cdg.ttl>

# optional
# add disease ontology set, like: NCIT
# wget
candig_repo add-ontology -n NCIT ga4gh-example-data/registry.db ncit.obo

# launch the server
# at different IP and/or port: ga4gh_server --host --port 8000
candig_server --host --port 8000 -c NoAuth

and then, from another terminal:

curl -X POST --header 'Content-Type: application/json' --header 'Accept: application/json' \ \
    | jq '.'


  "datasets": [
      "description": "PROFYLE test metadata",
      "id": "WyJQUk9GWUxFIl0",
      "name": "PROFYLE"

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