extras/Documentation/installation.md

In leeleavitt/procPharm: Constellation Pharmacology Data Analysis

Mac OS setup

If you are working on a Mac. First follow these instructions to set up your computer. Come back to this page when you have completed it.

General install

This Package allows you to view calcium imaging data along with visualize the cells. This package has not been released on CRAN yet, nor have the python components been released on PYPI.

To install the package on your home computer. First open R. If R is not installed make sure to install now here. While install select custom installation and select the multiple windows option.

# First install devtools to gain access to the function 
install.packages(c("devtools", "backports", "fs"))

On MAC, make sure to answer no, if prompted.

# Now install the package
devtools::install_github("https://github.com/leeleavitt/procPharm.git")

Make Sure to read the console if any ERROR's arise. If so Close R and paste the commands again.

Python Installation

This R package depends on some python processing. To install 1. Install the anaconda distribution. Make sure to select for a single user during this installation. From there you will need to use pip to install our software. 2. Now open the Anaconda Prompt, from your programs. This means click the windows logo and type anaconda prompt. Double click this and a terminal window will open. 3. Install git with

conda install git

1. Install the python package with,

pip install -e "git+https://github.com/leeleavitt/procPharm/#egg=pkg&subdirectory=python_packages/python_pharmer"

conda install scikit-image

1. Computer will need a restart after this

leeleavitt/procPharm documentation built on Feb. 3, 2021, 11:43 a.m.