Automation scripts¶

These small scripts keep each control computer in sync. They pull the latest protocols from GitHub every morning, push behavior data to the lab NAS every night, and update BpodAcademy and the DataJoint database.

All paths assume the user ratacad1 with everything under ~/ratacad/. Edit them to match your machine.

Schedule¶

Time	Script	What it does
01:00	`transferBpodData`	rsync `Bpod Local/Data` → NAS `RATACAD_DATA`; (Ubuntu) delete local files older than 30 days
08:00	`updateProtocols`	`git pull` the protocols repo, then mirror `Protocols/` into `Bpod Local/Protocols`
as needed	`updateBpodAcademy`	reinstall BpodAcademy from GitHub into the `bpod` conda env
as needed / cron on the DB host	`updateDJ`	reinstall `dj_ratacad` and run `dj-ratacad update` to ingest new sessions

Ubuntu¶

File	Download
`updateProtocols.sh`	download
`transferBpodData.sh`	download
`updateBpodAcademy.sh`	download
`updateDJ.sh`	download

updateProtocols.shtransferBpodData.shupdateBpodAcademy.shupdateDJ.sh

################################################
# bash script to update Bpod protocols directory
# from ScottLabBpodProtocols github
################################################

# navigate to ScottLabBpodProtocols directory
cd ~/ratacad/ScottLabBpodProtocols

# pull latest changes from master branch
#### uses SSH keys for github username = gkane26
git pull origin master

# sync ScottLabBpodProtocols/Protocols with local Bpod Protocols directory
rsync -avuz ~/ratacad/ScottLabBpodProtocols/Protocols ~/ratacad/Bpod\ Local/ --delete-after

#########################################
### transfer local Bpod Data to ENG drive
#########################################

rsync -avuz ~/ratacad/Bpod\ Local/Data/* /ad/eng/research/eng_research_scottlab/RATACAD_DATA
find ratacad/Bpod\ Local/Data -mtime +30 -type f -delete

##########################################
### update BpodAcademy pacakge from github
##########################################

source ~/anaconda3/etc/profile.d/conda.sh
conda activate bpod
pip uninstall -y bpod-academy
pip install git+ssh://git@github.com/RatAcad/BpodAcademy

#!/bin/bash
export RATACAD_DATA_DIR=/ad/eng/research/eng_research_scottlab/RATACAD_DATA
source ~/anaconda3/etc/profile.d/conda.sh
conda activate dj
pip uninstall -y dj-ratacad
pip install git+ssh://git@github.com/RatAcad/dj_ratacad
dj-ratacad update

transferBpodData.sh deletes local data

After copying, it deletes local data files older than 30 days (find ... -mtime +30 -delete). Check that the NAS copy is working before you enable it. The find path is relative, so it relies on cron running from the home directory (cron's default).

Windows¶

On Windows each .sh file is run by Cygwin through a matching .bat launcher, which is what Task Scheduler calls.

Script	`.sh`	`.bat`
updateProtocols	download	download
transferBpodData	download	download
transferMiniscopeData (optional, for miniscope rigs)	download	download

updateProtocols.shtransferBpodData.shtransferMiniscopeData.shlauncher (.bat)

cd /cygdrive/c/Users/ratacad1/ratacad/ScottLabBpodProtocols
git pull -f origin master
rsync -avuz /cygdrive/c/Users/ratacad1/ratacad/ScottLabBpodProtocols/Protocols /cygdrive/c/Users/ratacad1/ratacad/Bpod\ Local/ --delete-after

rsync -avuz --chmod=u+rwx,g+rwx /cygdrive/c/Users/ratacad1/ratacad/Bpod\ Local/Data/* /cygdrive/z/RATACAD_DATA

rsync -avuz --chmod=u+rwx,g+rwx /cygdrive/d/miniscope/* /cygdrive/z/MINISCOPE_DATA

C:\tools\cygwin\bin\mintty.exe /cygdrive/c/Users/ratacad1/ratacad/scripts/transferBpodData.sh