The aim of this project is to create software that can be used after running a 600s basal locomotion experiment using the Multi-worm tracker (Swierczek et al., 2011) to generate summary figures and statistics for that experiment.
This script also backs up experiment .zip files to a webdav server specified by the user.
Java
, R
, R packages ggplot2
, plyr
, stringr
, asbio
,and fmsb
, and the Multi-worm Tracker
Analysis software (Chore.jar
) as a shell script in the executable path named Chore
.
To "easily" do this on a Mac or Linux OS, please follow the following installation
instructions:
Install Homebrew by typing the following into the command line:
ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
Install the Multi-worm Tracker Analysis software via Homebrew to install Chore.jar and have it accesible as a shell script in the executable path named "Chore":
brew install homebrew/science/multi-worm-tracker
Install Linuxbrew by typing the following into the command line:
ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/linuxbrew/go/install)"
Put brew in your executable path by adding the commands below to either .bashrc
or
.zshrc
:
export PATH="$HOME/.linuxbrew/bin:$PATH"
export MANPATH="$HOME/.linuxbrew/share/man:$MANPATH"
export INFOPATH="$HOME/.linuxbrew/share/info:$INFOPATH"
Install the Multi-worm Tracker Analysis software via Homebrew to install Chore.jar and have it accesible as a shell script in the executable path named "Chore":
brew install homebrew/science/multi-worm-tracker
Set working directory to project's root directory
Call locomotion_driver.sh
from the Bash Shell
locomotion_driver.sh
requires the following arguments from the user: (1) webdav server
URL, (2) path on webdav where .zip
folders should be saved, and (3) the gigabytes of
memory to be devoted to the process (recommended as much as you have). See example below:
bash bin/locomotion_driver.sh https://webdav.server/location folder_to_backup_to 4