Usage Examples
DNAstack products can be accessed programmatically through the Command Line Interface (CLI) for Windows, Mac, and Linux environments.
For installation instructions, see the Installation page.
General
Set up a service registry
You can easily set up your environment by using the dnastack
use command. For example, we set up the CLI to work with the service endpoints available at viral.ai.
dnastack use viral.ai
Download Files / Blobs
dnastack files download [DRS-URL]
Arguments:
DRS-URL
: A DRS URL of the resource you would like to download
Example
dnastack files download drs://viral.ai/faux-blob-id-001 faux-blob-id-002
Collections
List Collections
dnastack collections list
List Collection Items
You can list all items in a particular collection with dnastack collections list-items -c SLUG_NAME
where SLUG_NAME
is the slug name of the collection. Here is an example.
dnastack collections list-items -c ncbi-sra
where items can be tables or blobs/files.
Query a Collection Table
dnastack collections query -c [SLUG-NAME] [COLLECTION-QUERY]
Arguments:
SLUG-NAME
: The name of the collection to query against
COLLECTION-QUERY
: The SQL query to execute
Example
dnastack collections query -c ncbi-sra "SELECT * FROM collections.ncbi_sra.variants LIMIT 10"
Alternatively, you can run the following query:
dnastack data-connect query --endpoint-id data-connect-ncbi-sra
"SELECT * FROM collections.ncbi_sra.variants LIMIT 10"
Additional Resources
Take a look at the GA4GH Data Connect Documentation for a detailed guide on using search commands.
Workbench
See the workbench reference for usage examples
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