Question: How can I automate file transfer after a Xenium run completes?
Answer: Modify the end-of-run script.
At the completion of each individual region within a Xenium run, the Xenium Onboard analysis calls the script $HOME/bin/endofrun.sh. Xenium users can edit the script to automate execution of actions, e.g. transfer of region results to network storage or notify a user the region data transfer is complete. Edits to the end-of-run flag script will persist through reboots and software updates.
Example commands:
#!/bin/bash
# shellcheck disable=SC2034
DONE_DIR=$1
### This script is executed after a run completes and can be used as
### part of your own automation.
###
### The $DONE_DIR var will contain the path to the completed directory
### contents and will have a format similar to:
### /output/20230330__223646__FOO_APT_a11/output-XETG00001__0007232__S1A_APT_V1__20230330_184300
### Where:
### RUN_DATE=20230330
### RUN_NAME=FOO_APT_a11
### REGION_NAME=S1A_APT_V1
### Example commands:
# cp -r "$DONE_DIR" /mnt/NFS_SHARE
# scp -r "$DONE_DIR" someuser@somehost:
# curl http://someserver/api/endpoint?run=finished
Related articles:
Products: Xenium Analyzer
Last Modified: 6/28/2023