将元数据摄取到candig存储库的例程
candig-ingest的Python项目详细描述
将元数据摄取到Candig1.0服务器的例程 需要[Candig服务器]（https://github.com/candig/candig-server）， [docopt]（http://docopt.readthedocs.io/en/latest/） 还有[熊猫]（https://github.com/pandas-dev/pandas）。
- 自由软件：GNU通用公共许可v3
您可以运行摄取，并使用生成的repo测试服务器，如下所示 （Candig服务器需要Python2.7<；1.0.0，Candig服务器需要Python3.6>；=1.0.0，请注意，当前不支持Python3.7。）
# Install virtualenv test_server # If you are running Python 2 python3 -m venv test_server # If you are running Python 3.6 cd test_server source bin/activate pip install --upgrade pip setuptools pip install candig-server # Specify anything <1.0.0 for Python 2.7, or >=1.0.0 for Python 3.6. pip install candig-ingest # 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: http://127.0.0.1:8001> # 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: https://www.ncbi.nlm.nih.gov/grc/human/ or http://genome.wustl.edu/pub/reference/ 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 "http://genome.wustl.edu/pub/reference/GRCh37-lite/GRCh37-lite.fa.gz"# 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 https://raw.githubusercontent.com/The-Sequence-Ontology/SO-Ontologies/master/so.obo 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 # https://github.com/ga4gh/ga4gh-server/blob/master/scripts/glue.py # https://github.com/ga4gh/ga4gh-server/blob/master/scripts/generate_gff3_db.py # ## download the relevant annotation release from Gencode # https://www.gencodegenes.org/releases/current.html # ## decompress # gunzip gencode.v27.annotation.gff3.gz # ## buid the annotation database # python generate_gff3_db.py -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 http://nif-crawler.neuinfo.org/monarch/ttl/cgd.ttl 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 http://purl.obolibrary.org/obo/ncit.obo 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 127.0.0.1 --port 8000 candig_server --host 127.0.0.1 --port 8000 -c NoAuth https://127.0.0.1:8000/
然后，从另一个终端：
curl -X POST --header 'Content-Type: application/json' --header 'Accept: application/json'\ http://127.0.0.1:8000/datasets/search \ | jq '.'
给予：
{"datasets":[{"description":"PROFYLE test metadata","id":"WyJQUk9GWUxFIl0","name":"PROFYLE"}]}
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