This script will allow you to delete studies from Genestack and their data in their S3 buckets.
Usage:
gs-delete {genestack|genestack-qc} TOKEN study_accession ...
You can specify either the genestack production server or the genestack-qc server. You'll need an API token with permission to delete those studies, and then you can provide multiple study accessions, such as GSF12345678.
Location:
This is in mercury's $PATH, so can just be run using gs-delete. It is recommended that it is run from mercury's $HOME however, becuase the logging file (.gs-delete.log) is relative to the location it is run from.
It's located in ~/genestack.
This script will upload data into S3, which will allow you to reference the files in the Genestack Uploader app.
Usage:
gs-upload [-qc] PROJET_NAME FILE ...
By default, will upload to the main Genestack bucket for use on the main Genestack isntance, although the -qc flag can be used to upload it to the qc bucket for that instance.
The project name is purely for organisation within the bucket. You can specify multiple files, and glob patterns are allowed.
Location:
This is in mercury's $PATH, so can be just run using gs-upload. (It is located/symliked in /software/hgi/installs/genestack/bin/).
There's a full description on the Confluence page for the Genestack Uploader app.
This script allows you to change the owner of studies in Genestack.
Usage:
./change-owner.sh CURRENT_OWNER_EMAIL NEW_OWNER_EMAIL
Note: This will transfer all studies owned by CURRENT_OWNER_EMAIL to be owned by NEW_OWNER_EMAIL
Note: This is based off e-mail addresses. It executes the SQL script .change_owner.sql which was provided to us by Genestack.
Warning: Before transfer, the study must be shared with the user it is being transferred to, otherwise they won't be able to see it.
Location: This script must be run on the instance running the Genestack containers for the instance you're updating. This is because it has to execute in the database container, and restart the backend continaer (to clear the cache).
Logging: This script logs to ~/.audit.gs_owner, logging the transfer that happened, and the output from the SQL. This output can be used to reverse the change if neccesary.
This script will allow to rollback a change made by change-owner.sh.
Usage:
./rollback-owner-change.sh TIMESTAMP
where TIMESTAMP is the timestamp tagged onto the files logged by the original script in the auditing directory.
Note: This needs to find the logged files from that run, so make sure they exist.
Location: This script must be run on the instance running the Genestack containers for the instance you're updating. This is because it has to execute in the database container, and restart the backend container (to clear the cache).
Logging: This script logs to ~/.audit.gs_owner, logging the revertion that happened.
This script will backup* all the data in the two Genestack S3 buckets, genestackupload and genestackuploadtest.
It is copied to /lustre and IRODS.
This can be run as a frequent cronjob. It will rclone sync the buckets to directories in DIR defined at the top, (at the end we run chmod -R o-rwx on this area). If there is a change, it'll create a new backup in $DIR - this is a .tar.gz file with the datetime it was created as the title.
It will then copy the latest backups to IRODS, in the location defined by $IRODS_LOC at the top.
Finally, assuming there are at least 6 backups from the last 6 months, it'll delete any of these backups older than 6 months.
Location: this is intended to be run as mercury on hgi-farm5, hence defining the $PATH to include the latest version of rclone, and using /usr/bin/find to use the -delete flag, so we're not hindered by the armed environment.
We also need gs-public and gs-private in the $PATH
see README in ./delete-template/ folder