Index

Symbols

--api-key gencove-basespace-autoimports-create command line option gencove-basespace-autoimports-list command line option gencove-basespace-biosamples-list command line option gencove-basespace-projects-import command line option gencove-basespace-projects-list command line option gencove-download command line option gencove-projects-create command line option gencove-projects-create-batch command line option gencove-projects-create-merged-vcf command line option gencove-projects-delete-samples command line option gencove-projects-get-batch command line option gencove-projects-get-merged-vcf command line option gencove-projects-import-existing-samples command line option gencove-projects-list command line option gencove-projects-list-batch-types command line option gencove-projects-list-batches command line option gencove-projects-list-pipeline-capabilities command line option gencove-projects-list-pipelines command line option gencove-projects-list-samples command line option gencove-projects-restore-samples command line option gencove-projects-run-prefix command line option gencove-projects-status-merged-vcf command line option gencove-s3-autoimports-create command line option gencove-s3-autoimports-list command line option gencove-s3-import command line option gencove-samples-download-file command line option gencove-samples-get-metadata command line option gencove-samples-set-metadata command line option gencove-upload command line option gencove-uploads-list command line option --archive-status gencove-projects-list-samples command line option --batch-name gencove-projects-create-batch command line option --batch-type gencove-projects-create-batch command line option --checksum gencove-samples-download-file command line option --checksums gencove-download command line option --download-template gencove-download command line option --download-urls gencove-download command line option --email gencove-basespace-autoimports-create command line option gencove-basespace-autoimports-list command line option gencove-basespace-biosamples-list command line option gencove-basespace-projects-import command line option gencove-basespace-projects-list command line option gencove-download command line option gencove-projects-create command line option gencove-projects-create-batch command line option gencove-projects-create-merged-vcf command line option gencove-projects-delete-samples command line option gencove-projects-get-batch command line option gencove-projects-get-merged-vcf command line option gencove-projects-import-existing-samples command line option gencove-projects-list command line option gencove-projects-list-batch-types command line option gencove-projects-list-batches command line option gencove-projects-list-pipeline-capabilities command line option gencove-projects-list-pipelines command line option gencove-projects-list-samples command line option gencove-projects-restore-samples command line option gencove-projects-run-prefix command line option gencove-projects-status-merged-vcf command line option gencove-s3-autoimports-create command line option gencove-s3-autoimports-list command line option gencove-s3-import command line option gencove-samples-download-file command line option gencove-samples-get-metadata command line option gencove-samples-set-metadata command line option gencove-upload command line option gencove-uploads-list command line option --file-types gencove-download command line option --host gencove-basespace-autoimports-create command line option gencove-basespace-autoimports-list command line option gencove-basespace-biosamples-list command line option gencove-basespace-projects-import command line option gencove-basespace-projects-list command line option gencove-download command line option gencove-projects-create command line option gencove-projects-create-batch command line option gencove-projects-create-merged-vcf command line option gencove-projects-delete-samples command line option gencove-projects-get-batch command line option gencove-projects-get-merged-vcf command line option gencove-projects-import-existing-samples command line option gencove-projects-list command line option gencove-projects-list-batch-types command line option gencove-projects-list-batches command line option gencove-projects-list-pipeline-capabilities command line option gencove-projects-list-pipelines command line option gencove-projects-list-samples command line option gencove-projects-restore-samples command line option gencove-projects-run-prefix command line option gencove-projects-status-merged-vcf command line option gencove-s3-autoimports-create command line option gencove-s3-autoimports-list command line option gencove-s3-import command line option gencove-samples-download-file command line option gencove-samples-get-metadata command line option gencove-samples-set-metadata command line option gencove-upload command line option gencove-uploads-list command line option

--json gencove-samples-set-metadata command line option --metadata gencove-upload command line option --metadata-json gencove-basespace-autoimports-create command line option gencove-basespace-projects-import command line option gencove-projects-import-existing-samples command line option gencove-projects-run-prefix command line option gencove-s3-autoimports-create command line option gencove-s3-import command line option --no-progress gencove-download command line option gencove-projects-get-batch command line option gencove-projects-get-merged-vcf command line option gencove-samples-download-file command line option gencove-upload command line option --no-skip-existing gencove-download command line option --output gencove-upload command line option --output-filename gencove-projects-get-batch command line option gencove-projects-get-merged-vcf command line option gencove-samples-get-metadata command line option --password gencove-basespace-autoimports-create command line option gencove-basespace-autoimports-list command line option gencove-basespace-biosamples-list command line option gencove-basespace-projects-import command line option gencove-basespace-projects-list command line option gencove-download command line option gencove-projects-create command line option gencove-projects-create-batch command line option gencove-projects-create-merged-vcf command line option gencove-projects-delete-samples command line option gencove-projects-get-batch command line option gencove-projects-get-merged-vcf command line option gencove-projects-import-existing-samples command line option gencove-projects-list command line option gencove-projects-list-batch-types command line option gencove-projects-list-batches command line option gencove-projects-list-pipeline-capabilities command line option gencove-projects-list-pipelines command line option gencove-projects-list-samples command line option gencove-projects-restore-samples command line option gencove-projects-run-prefix command line option gencove-projects-status-merged-vcf command line option gencove-s3-autoimports-create command line option gencove-s3-autoimports-list command line option gencove-s3-import command line option gencove-samples-download-file command line option gencove-samples-get-metadata command line option gencove-samples-set-metadata command line option gencove-upload command line option gencove-uploads-list command line option --project-id gencove-download command line option --run-project-id gencove-upload command line option --sample-ids gencove-download command line option gencove-projects-create-batch command line option gencove-projects-delete-samples command line option gencove-projects-import-existing-samples command line option gencove-projects-restore-samples command line option --search gencove-projects-list-samples command line option gencove-uploads-list command line option --skip-existing gencove-download command line option --status gencove-projects-list-samples command line option gencove-projects-run-prefix command line option gencove-uploads-list command line option --version gencove command line option

B

BASESPACE_PROJECT_ID gencove-basespace-biosamples-list command line option BASESPACE_PROJECT_IDS gencove-basespace-projects-import command line option

BATCH_ID gencove-projects-get-batch command line option

D

DESTINATION gencove-download command line option gencove-samples-download-file command line option gencove-upload command line option

F

FILE_TYPE gencove-samples-download-file command line option

G

gencove command line option --version gencove-basespace-autoimports-create command line option --api-key --email --host --metadata-json --password IDENTIFIER PROJECT_ID gencove-basespace-autoimports-list command line option --api-key --email --host --password gencove-basespace-biosamples-list command line option --api-key --email --host --password BASESPACE_PROJECT_ID gencove-basespace-projects-import command line option --api-key --email --host --metadata-json --password BASESPACE_PROJECT_IDS PROJECT_ID gencove-basespace-projects-list command line option --api-key --email --host --password gencove-download command line option --api-key --checksums --download-template --download-urls --email --file-types --host --no-progress --no-skip-existing --password --project-id --sample-ids --skip-existing DESTINATION gencove-projects-create command line option --api-key --email --host --password PIPELINE_CAPABILITY_ID PROJECT_NAME gencove-projects-create-batch command line option --api-key --batch-name --batch-type --email --host --password --sample-ids PROJECT_ID gencove-projects-create-merged-vcf command line option --api-key --email --host --password PROJECT_ID gencove-projects-delete-samples command line option --api-key --email --host --password --sample-ids PROJECT_ID gencove-projects-get-batch command line option --api-key --email --host --no-progress --output-filename --password BATCH_ID gencove-projects-get-merged-vcf command line option --api-key --email --host --no-progress --output-filename --password PROJECT_ID gencove-projects-import-existing-samples command line option --api-key --email --host --metadata-json --password --sample-ids PROJECT_ID gencove-projects-list command line option --api-key --email --host --password gencove-projects-list-batch-types command line option --api-key --email --host --password PROJECT_ID gencove-projects-list-batches command line option --api-key --email --host --password PROJECT_ID

gencove-projects-list-pipeline-capabilities command line option --api-key --email --host --password PIPELINE_ID gencove-projects-list-pipelines command line option --api-key --email --host --password gencove-projects-list-samples command line option --api-key --archive-status --email --host --password --search --status PROJECT_ID gencove-projects-restore-samples command line option --api-key --email --host --password --sample-ids PROJECT_ID gencove-projects-run-prefix command line option --api-key --email --host --metadata-json --password --status PREFIX PROJECT_ID gencove-projects-status-merged-vcf command line option --api-key --email --host --password PROJECT_ID gencove-s3-autoimports-create command line option --api-key --email --host --metadata-json --password PROJECT_ID S3_URI gencove-s3-autoimports-list command line option --api-key --email --host --password gencove-s3-import command line option --api-key --email --host --metadata-json --password PROJECT_ID S3_URI gencove-samples-download-file command line option --api-key --checksum --email --host --no-progress --password DESTINATION FILE_TYPE SAMPLE_ID gencove-samples-get-metadata command line option --api-key --email --host --output-filename --password SAMPLE_ID gencove-samples-set-metadata command line option --api-key --email --host --json --password SAMPLE_ID gencove-upload command line option --api-key --email --host --metadata --no-progress --output --password --run-project-id DESTINATION SOURCE gencove-uploads-list command line option --api-key --email --host --password --search --status gencove-webhooks-verify command line option HEADER PAYLOAD SECRET gencove.cli module

H

HEADER gencove-webhooks-verify command line option

I

IDENTIFIER gencove-basespace-autoimports-create command line option

M

module gencove.cli

P

PAYLOAD gencove-webhooks-verify command line option PIPELINE_CAPABILITY_ID gencove-projects-create command line option PIPELINE_ID gencove-projects-list-pipeline-capabilities command line option PREFIX gencove-projects-run-prefix command line option PROJECT_ID gencove-basespace-autoimports-create command line option gencove-basespace-projects-import command line option gencove-projects-create-batch command line option gencove-projects-create-merged-vcf command line option gencove-projects-delete-samples command line option gencove-projects-get-merged-vcf command line option gencove-projects-import-existing-samples command line option gencove-projects-list-batch-types command line option gencove-projects-list-batches command line option gencove-projects-list-samples command line option gencove-projects-restore-samples command line option gencove-projects-run-prefix command line option gencove-projects-status-merged-vcf command line option gencove-s3-autoimports-create command line option gencove-s3-import command line option

PROJECT_NAME gencove-projects-create command line option

S

S3_URI gencove-s3-autoimports-create command line option gencove-s3-import command line option SAMPLE_ID gencove-samples-download-file command line option gencove-samples-get-metadata command line option gencove-samples-set-metadata command line option

SECRET gencove-webhooks-verify command line option SOURCE gencove-upload command line option