Computational Basics
Useful information for new/non-programmers
This section details installation of high level dependencies: Git Bash (Windows users), git, and Anaconda. If you have installed and are familiar with these items, you can skip this section and move on to Installation. Installation on Linux is not detailed here, as we just assume you know what you’re doing. Once this section is completed, continue to installation.
Installing Git
Windows users
Install Git/Git Bash by following the instructions here. Unless you know what you’re doing, sticking to the default options during install is best.
Mac users
Install Git by following the instructions here, if not already installed on your machine. Some commands must be performed through the terminal. You can open a terminal by typing command + spacebar to open Spotlight Search, then type “Terminal”; opening the search result will give you a terminal window.
Opening a Terminal Window
Later steps in our installation will require you to write commands in terminal. To open a terminal in Windows, right-click on either the desktop background or within your file explorer, then open Git Bash. For Mac users, type command + spacebar, search “Terminal”, then open the search result.
Installing Anaconda
Anaconda is an open-source package managment framework for scientific computing with Python. For details, look at their website here. All software that supports evSeq is or can be handled by the Anaconda package manager. See below for installation instructions on both Windows and Mac.
Windows users
Install Anaconda following the instructions here. At step 8, we recommend adding Anaconda to your PATH environment variable. Note that this is in contrast to the recommendation of Anaconda, but their concerns shouldn’t apply for this use case. Once installation is complete, open a terminal window and enter the below command
conda init bash
Mac users
Install Anaconda following the instructions here.
Construction of a Folder for holding Git repositories
The next step will be to install evSeq, as described in Installation. The recommended way involves cloning the evSeq repository from GitHub. If you have not worked with Git repos before, we recommend creating a folder where you can store all of them. Wherever seems reasonable to you (most likely your home directory), create a folder called git_repos or GitRepos or whatever seems best for you. Navigate to this folder and perform installation from there.
As an example from the command line, you would perform the following to make a folder named git_repos:
# Change directories (cd) to your home directory (~)
cd ~
# Make the directory (mkdir) named 'git_repos'
mkdir git_repos
# Change directories to this new directory
cd git_repos
From here you will clone the evSeq repository and then install it as described on the next page.
Next page: Installation.
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