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        "author": "CanDIG team",
        "author_email": "info@distributedgenomics.ca",
        "bugtrack_url": null,
        "classifiers": [
            "Natural Language :: English",
            "Programming Language :: Python :: 3.6",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
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        "description": "==============\nCanDIG-ingest\n==============\n\nRoutines for ingesting metadata into a CanDIG 1.0 server\nRequires [candig-server](https://github.com/candig/candig-server),\n[docopt](http://docopt.readthedocs.io/en/latest/)\nand [pandas](https://github.com/pandas-dev/pandas).\n\n* Free software: GNU General Public License v3\n\n\nYou can run the ingestion and test a server with the resulting repo as follows \n(requires Python 2.7 for candig-server<1.0.0, or Python 3.6 for candig-server>=1.0.0, note that Python 3.7 is not currently supported.)\n\n.. code:: bash\n\n    # Install\n    virtualenv test_server # If you are running Python 2\n    python3 -m venv test_server # If you are running Python 3.6\n\n    cd test_server\n    source bin/activate\n    pip install --upgrade pip setuptools\n    pip install candig-server # Specify anything <1.0.0 for Python 2.7, or >=1.0.0 for Python 3.6.\n    pip install candig-ingest\n\n    # ingest data and make the repo\n    mkdir candig-example-data\n    ingest candig-example-data/registry.db <path to example data, like: mock_data/clinical_metadata_tier1.json>\n\n    # optional\n    # add peer site addresses\n    candig_repo add-peer candig-example-data/registry.db <peer site IP address, like: http://127.0.0.1:8001>\n\n    # optional\n    # create dataset for reads and variants\n    candig_repo add-dataset --description \"Reads and variants dataset\" candig-example-data/registry.db read_and_variats_dataset\n\n    # optinal\n    # add reference set, data source: https://www.ncbi.nlm.nih.gov/grc/human/ or http://genome.wustl.edu/pub/reference/\n    candig_repo add-referenceset candig-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\"\n\n    # optional\n    # add reads\n    candig_repo add-readgroupset -r -I <path to bam index file> -R GRCh37-lite candig-example-data/registry.db read_and_variats_dataset <path to bam file>\n\n    # optional\n    # add variants\n    candig_repo add-variantset -I <path to variants index file> -R GRCh37-lite candig-example-data/registry.db read_and_variats_dataset <path to vcf file>\n\n    # optional\n    # add sequence ontology set\n    # wget https://raw.githubusercontent.com/The-Sequence-Ontology/SO-Ontologies/master/so.obo\n    candig_repo add-ontology candig-example-data/registry.db <path to sequence ontology set, like: so.obo> -n so-xp\n\n    # optional\n    # add features/annotations\n    #\n    ## get the following scripts\n    # https://github.com/ga4gh/ga4gh-server/blob/master/scripts/glue.py\n    # https://github.com/ga4gh/ga4gh-server/blob/master/scripts/generate_gff3_db.py\n    #\n    ## download the relevant annotation release from Gencode\n    # https://www.gencodegenes.org/releases/current.html\n    #\n    ## decompress\n    # gunzip gencode.v27.annotation.gff3.gz\n    #\n    ## build the annotation database\n    # python generate_gff3_db.py -i gencode.v27.annotation.gff3 -o gencode.v27.annotation.db -v    \n    #\n    # build index for your annotation database\n    # Run \"CREATE INDEX name_type_index ON FEATURE (gene_name, type)\" in Sqlite browser\n    #\n    # add featureset\n    candig_repo add-featureset candig-example-data/registry.db read_and_variats_dataset <path to the annotation.db> -R GRCh37-lite -O so-xp\n\n    # optional\n    # add phenotype association set from Monarch Initiative\n    # wget http://nif-crawler.neuinfo.org/monarch/ttl/cgd.ttl\n    candig_repo add-phenotypeassociationset candig-example-data/registry.db read_and_variats_dataset <path to the folder containing cdg.ttl>\n\n    # optional\n    # add disease ontology set, like: NCIT\n    # wget http://purl.obolibrary.org/obo/ncit.obo\n    candig_repo add-ontology -n NCIT candig-example-data/registry.db ncit.obo\n\n    # launch the server at different IP and/or port:\n    candig_server --host 127.0.0.1 --port 8000 -c NoAuth\n\n\n    http://127.0.0.1:8000/\n\n\nand then, from another terminal:\n\n.. code:: bash\n\n    curl -X POST --header 'Content-Type: application/json' --header 'Accept: application/json' \\\n        http://127.0.0.1:8000/datasets/search \\\n        | jq '.'\n\ngiving:\n\n.. code:: JSON\n\n    {\n      \"datasets\": [\n        {\n          \"description\": \"PROFYLE test metadata\",\n          \"id\": \"WyJQUk9GWUxFIl0\",\n          \"name\": \"PROFYLE\"\n        }\n      ]\n    }\n\n\n\n",
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        "keywords": "candig-ingest",
        "license": "GNU General Public License v3",
        "maintainer": "",
        "maintainer_email": "",
        "name": "candig-ingest",
        "package_url": "https://pypi.org/project/candig-ingest/",
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        "summary": "Routines for ingesting metadata to a CanDIG repository",
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