ga4gh / ga4gh/cloud-interop-testing
Add WES and Discovery Search to FASP Python examples
- Dominant language
- Python
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- 9
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Description
https://github.com/ianfore/FASPclient has example python code to
1. query data
2. obtain urls via DRS
3. run a compute
It currently queries BigQuery directly and submits a pipelines directly to GCP Life Sciences pipeline.
We want to convert the script so steps 1 and 3 use the equivalent GA4GH APIs.
Creating issue here to track the following
- [x] Modify FASPScript1.py to submit jobs via WES instead of Life Sciences Pipeline
- Make BigQuery datasets searchable through Discovery Search
- [x] 1000Genomes
- [ ] COPDGene
- [ ] GECCO
- [x] Modify FASPScript1.py to use Discovery Search API to search the data
- [ ] Create scrambled/fake versions of COPDGene, GECCO
- [ ] Put DiscoverySearch datasets under authentication and authorization – stretch?
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