Bootcamp

GENERAL INFORMATION TOP

Those not familiar with the UNIX shell, please read: http://swcarpentry.github.io/shell-novice/

Those not familiar with R, please see the following videos:

Windows users only: Please make sure your machine is in Developer Mode such that you can access a command line interface to use bash on Ubuntu on Windows. Instructions on how to do this are provided here: https://www.windowscentral.com/how-install-bash-shell-command-line-windows-10

Please email Molly Rathbun if you have any questions or problems during installations.

The last session on Monday will cover the technical requirements for the following days.

GIT AND GITHUB TOP

Install git

Install git on Windows

Download the Git for Windows installer.
Run the installer and follow the steps bellow:
1. Click on Next until you get to the step below.
2. Select Use Git from the Windows Command Prompt and click on Next.
3. Click on Next. Keep Checkout Windows-style, commit Unix-style line endings selected.
4. Select Use Windows' default console window and click on Next.
5. Click on Next then Finish.
Video Tutorial

This will provide you with both Git and Bash in the Git Bash program. If you make a mistake you may rerun the installer and select the appropriate options.

Install git on Mac OSX

Git is installed by default on the newest MacOSX.

If that is not the case you may use conda to install git or to set up just git alone see:

For OS X 10.9 and higher, install Git for Mac by downloading and running the most recent mavericks installer from this list.

After installing Git, there will not be anything in your /Applications folder, as Git is a command line program. For older versions of OS X (10.5-10.8) use the most recent available installer labelled snow-leopard available here.

Install git on Linux

If Git is not already available on your machine you can try to install it via your distro's package manager. For Debian/Ubuntu run sudo apt-get install git and for Fedora run sudo yum install git.

Create a GitHub account

Git is a version control system that lets you track who made changes to what when and has options for easily updating a shared or public version of your code on github.com. You will need a supported web browser (current versions of Chrome, Firefox or Safari, or Internet Explorer version 9 or above).

You will need an account at github.com for parts of the Git lesson. Basic GitHub accounts are free. We encourage you to create a GitHub account if you don't have one already. Please consider what personal information you'd like to reveal. For example, you may want to review these instructions for keeping your email address private provided at GitHub.

Install Github Desktop

Github Desktop is a standalone interface for interacting with Github repos. Install from here.

Set up SSH passwords

ssh-keygen

This will generate a password in ~/.ssh/id_rsa.pub

cat ~/.ssh/id_rsa.pub

Copy and paste the key into the Github -> Account -> Settings -> Add SSH key

Common git commands

Command we typically do once:

git clone <uri> - clones a remote repository
git add <filepath> - adds a file to git tracking

Commands we use all the time:

git status - what is the current status of the repository
git diff - what has changed since the last commit
git push <uri> - push the changes to remote
git pull <uri> - pull and merge remote

Further information:

Git related lessons on Software Carpentry

R AND RSTUDIO TOP

How to install R

For simulation we are going to use R, a statistical programming language. The software is open-source, interacts well with git, has many packages written by and for the bioinformatics community and is also useful for developing graphics and web app.

We are going to access R via a package called RStudio, which provides additional resources including a window system which facilitates installing packages , accessing the help files, and documenting your work. RStudio is also free.

All of this software is available on Macs, Windows, and Linux. Mostly it works identically on all types of computers, although I have noticed that sometimes the versions are out of sync.

To get started, please install R and RStudio as directed below.

Installing R

Go to https://www.r-project.org/
Select a CRAN mirror. (This is the computer that you are downloading from. It is advisable to select a mirror that is geographically close.)
Select the appropriate version for the type of computer you are using.
Install the downloaded software just like any other software on your computer.

Installing RStudio

Go to https://www.rstudio.com/
Click on the Download button.
Scroll down to "Download R Studio Desktop".
Select the appropriate installer.
Install the downloaded software.

Check the download

Click on the R Studio icon. This should open R Studio.

SHELL TOP

Install Bash terminals

(install instructions copied from Software Carpentry)

Mac OS

For a Mac computer, the default Unix Shell is Bash, and it is available via the Terminal Utilities program within your Applications folder. To open Terminal, try one or both of the following:

Go to your Applications. Within Applications, open the Utilities folder. Locate Terminal in the Utilities folder and open it.
Use the Mac ‘Spotlight’ computer search function. Search for: Terminal and press Return.

How to Use Terminal on a Mac

Windows

Computers with Windows operating systems do not automatically have a Unix Shell program installed. In this lesson, we encourage you to turn on Developer Mode in Windows such that you can access a command line interface to use bash on Ubuntu on Windows. An alternative is to use the shell emulator included in Git for Windows, which gives you access to both Bash shell commands and Git. If you are attending a Software Carpentry workshop session, it is likely you have already received instructions on how to install Git for Windows. Once installed, you can open a terminal by running the program Git Bash from the Windows start menu.

How to Install Bash shell command-line tool on Windows 10 Install and Use the Linux Bash Shell on Windows 10

You could also install PuTTY for accessing remote servers, but this is not required in the 2019 workshop.

Note for navigating directories in Bash on Mac vs. Windows

When navigating file directories in Bash you will use the command cd however, the input is slightly different between Mac and Windows. For example, to access my desktop from the CLI on Mac, I will type cd /Users/mollyrathbun/Desktop/. On Windows, the command is the same, but the directory structure is slightly different: cd mnt/c/Users/mollyrathbun/Desktop/.

EDITOR TOP

Install a text editor

Microsoft Word is NOT a text editor. Using Word to edit text will will eventually cause (devious) errors. Best if you start using a proper text editor. Essential features:

Ability to show TAB characters versus multiple SPACE characters. Mixing up TABS and SPACES is a very common error. Copy-pasting from a web page often turns a TAB into SPACE characters (yes, it very annoying!) You need the ability to see the difference between these otherwise invisible characters if necessary.
Show line numbering. Allows you to identify the line where an error is reported.
Switch line endings. Line endings have variants: Unix, Windows or Mac OS 9 endings (the new Mac OSX uses Unix line endings). Typically all files should have a Unix line ending mode. Your editor needs to have the ability to convert line endings to Unix format.

Recommendations

Notepad++ on Windows
Sublime Text on most other platforms

Personal preference :

PyCharm is a Python programming specific editor with very powerful features.

Install pandoc

Pandoc can convert documents across formats: markdown to html or pdf etc.

On Mac OSX:

brew install pandoc

On windows visit the Pandoc website.

Software Installation