farmer

Slack bot that tells you the status of your LSF jobs 🧑‍🌾

Usage

Farmer currently has two functions: listing pending/running jobs, and notifying you when your jobs finish.

To see your pending/running jobs, send Farmer a message saying "jobs". (You can also see jobs for other users, e.g. by saying "jobs for cellgeni-su".)

To be notified when jobs finish, you can use the included post-exec script:

$ bsub ... -Ep /software/cellgen/cellgeni/etc/notify-slack.sh

or as a bsub comment:

#BSUB -Ep /software/cellgen/cellgeni/etc/notify-slack.sh

If you submit an array job with this post-exec script, you'll only be notified once every job in the array has finished.

Preemptively Answered Questions

• I don't use bsub, I use Nextflow – Nextflow has built-in support for sending notifications when jobs finish. For example: nextflow run -N [email protected]

• I don't use bsub, I use wr – when adding a command to wr, use a command line like: wr add --on_exit "[{\"run\": \"/software/cellgen/cellgeni/etc/notify-slack.sh --user=$USER --label='wr job'\"}, {\"cleanup\": true}]", replacing the job label as appropriate.

  If you want to be notified only when a group of wr jobs has completed, add a job to send the notification (it will run once immediately):

  $ echo "/software/cellgen/cellgeni/etc/notify-slack.sh --user=$USER --label='wr jobs'" | wr add --deps notify

  Then add your jobs to the notify dependency group, using a command like wr add --dep_grps notify. Note that you only need to run wr add --deps notify once – it will automatically notify you again if you add more commands with --dep_grps notify in the future.

  (Remember to replace $USER in the above commands with your own username, if you're using a service account.)

• I run jobs using a service account/I need Slack notifications to go to someone else – by default, Farmer tries to find a Slack account belonging to the job's owner, but you can override this heuristic in two ways.

  One option is to set the environment variable FARMER_SLACK_USER to your username: for example, put export FARMER_SLACK_USER=zz0 into your service account's ~/.bashrc. This might be useful if you run many jobs using this service account.

  Alternatively, you can pass a username straight to the post-exec script, by adding quotes (this overrides the environment variable, if set):

  $ bsub ... -Ep "/software/cellgen/cellgeni/etc/notify-slack.sh zz0"

Development

See HACKING.md.