import_seq_results.py

Checks DNAnexus for new sequencing result projects and imports metadata (i.e. number of reads) into Pulsar by creating a SequencingRun object if necessary and one or more SequencingResult objects.

See wiki documentation in the pulsar_lims GitHub repo at https://github.com/nathankw/pulsar_lims/wiki/Importing-Sequencing-Results.

If the –log-s3 flag is set, then the log files will be uploaded to S3 in the bucket specified by the environment variable PULSARPYDX_S3. The log files will be stored in this bucket by timestamp.

usage: import_seq_results.py [-h] [-d DAYS_AGO] [--log-s3]

Named Arguments

-d, --days-ago	The number of days ago to query for new projects that are billed to org-snyder_encode. Default: 30
--log-s3	Presence of this option means to upload the log files to the S3 bucket indicated by the environment variable PULSARPYDX_S3. Default: False