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.
To help ensure complete data transfers, it is recommended to use commands that copy folders to the destination as opposed to moving them.
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