Software Installation

GIT AND GITHUB TOP

## Content 1. [ Install git ](#install-git) 1. [ Install git ](#install-git) --- ## Install git ### Install git on Windows 1. Download the [Git for Windows][wingit] installer. 1. Run the installer and follow the steps bellow: 1. Click on `Next` until you get to the step below. 1. Select `Use Git from the Windows Command Prompt` and click on `Next`. 1. Click on `Next`. Keep `Checkout Windows-style, commit Unix-style line endings` selected. 1. Select `Use Windows' default console window` and click on `Next`. 1. Click on `Next` then `Finish`. 1. [Video Tutorial][wingit-video] 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. [wingit-video]: https://www.youtube.com/watch?v=339AEqk9c-8 [wingit]: https://git-for-windows.github.io/ --- ### 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: 1. [Git downloads][gitdownload] 1. [Video Tutorial][macgit-video] [gitdownload]: https://git-scm.com/downloads [handbook]: https://www.biostarhandbook.com/book/computer/get-ready.html 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. [macgit-video]: https://www.youtube.com/watch?v=9LQhwETCdwY --- ### 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][github]. 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][github] 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](https://desktop.github.com/). ### 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 ` - clones a remote repository * `git add ` - 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 ` - push the changes to remote * `git pull ` - pull and merge remote Further information: * [Git related lessons on Software Carpentry][lessons] [lessons]:http://software-carpentry.org/lessons/ [github]: https://www.github.com

« back to top

## Install git ### Install git on Windows 1. Download the [Git for Windows][wingit] installer. 1. Run the installer and follow the steps bellow: 1. Click on `Next` until you get to the step below. 1. Select `Use Git from the Windows Command Prompt` and click on `Next`. 1. Click on `Next`. Keep `Checkout Windows-style, commit Unix-style line endings` selected. 1. Select `Use Windows' default console window` and click on `Next`. 1. Click on `Next` then `Finish`. 1. [Video Tutorial][wingit-video] 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. [wingit-video]: https://www.youtube.com/watch?v=339AEqk9c-8 [wingit]: https://git-for-windows.github.io/ --- ### Install git on Mac OSX To fully set up your Mac for bioinformatics we recommend the [Biostar Handbook][handbook] website. Alternatively to set up just git alone see: 1. [Git downloads][gitdownload] 1. [Video Tutorial][macgit-video] [gitdownload]: https://git-scm.com/downloads [handbook]: https://www.biostarhandbook.com/book/computer/get-ready.html 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. [macgit-video]: https://www.youtube.com/watch?v=9LQhwETCdwY --- ### 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][github]. 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][github] 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. ### 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 ` - clones a remote repository * `git add ` - 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 ` - push the changes to remote * `git pull ` - pull and merge remote Further information: * [Git related lessons on Software Carpentry][lessons] [lessons]:http://software-carpentry.org/lessons/ [github]: https://www.github.com

« back to top

R AND RSTUDIO TOP

## Content 1. [ How to install R ](#how-to-install-r) 1. [ How to install R ](#how-to-install-r) --- ## 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 1. Go to 2. Select a CRAN mirror. (This is the computer that you are downloading from. It is advisable to select a mirror that is geographically close.) 3. Select the appropriate version for the type of computer you are using. 4. Install the downloaded software just like any other software on your computer. ### Installing RStudio 1. Go to 2. Click on the Download button. 3. Scroll down to "Download R Studio Desktop". 4. Select the appropriate installer. 5. Install the downloaded software. ### Check the download Click on the R Studio icon. This should open R Studio.

« back to 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 1. Go to 2. Select a CRAN mirror. (This is the computer that you are downloading from. It is advisable to select a mirror that is geographically close.) 3. Select the appropriate version for the type of computer you are using. 4. Install the downloaded software just like any other software on your computer. ### Installing RStudio 1. Go to 2. Click on the Download button. 3. Scroll down to "Download R Studio Desktop". 4. Select the appropriate installer. 5. Install the downloaded software. ### Check the download Click on the R Studio icon. This should open R Studio.

« back to top

SHELL TOP

## Content 1. [ Install Bash terminals ](#install-bash-terminals) 1. [ Install Bash terminals ](#install-bash-terminals) --- ## Install Bash terminals (install instructions copied from [Software Carpentry][swcsetup]) [swcsetup]: http://swcarpentry.github.io/shell-novice/setup.html ### 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: 1. Go to your Applications. Within Applications, open the Utilities folder. Locate Terminal in the Utilities folder and open it. 1. Use the Mac ‘Spotlight’ computer search function. Search for: Terminal and press Return. [How to Use Terminal on a Mac][macterm] [macterm]: http://www.macworld.co.uk/feature/mac-software/how-use-terminal-on-mac-3608274] ### 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](https://www.windowscentral.com/how-install-bash-shell-command-line-windows-10) 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][win10bashinstall] [Install and Use the Linux Bash Shell on Windows 10][win10bashuse] [win10bashinstall]: https://www.windowscentral.com/how-install-bash-shell-command-line-windows-10 [win10bashuse]: https://www.howtogeek.com/249966/how-to-install-and-use-the-linux-bash-shell-on-windows-10 You could also [install PuTTY][putty] for accessing remote servers, but this is not required in the 2019 workshop. [putty]: https://www.putty.org/ ### 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/`.

« back to top

## Install Bash terminals (install instructions copied from [Software Carpentry][swcsetup]) [swcsetup]: http://swcarpentry.github.io/shell-novice/setup.html ### 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: 1. Go to your Applications. Within Applications, open the Utilities folder. Locate Terminal in the Utilities folder and open it. 1. Use the Mac ‘Spotlight’ computer search function. Search for: Terminal and press Return. [How to Use Terminal on a Mac][macterm] [macterm]: http://www.macworld.co.uk/feature/mac-software/how-use-terminal-on-mac-3608274] ### Windows Computers with Windows operating systems do not automatically have a Unix Shell program installed. In this lesson, we encourage you to use an 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. Other solutions are available for running Bash commands on Windows. There is now a Bash shell command-line tool available for Windows 10. Additionally, you can run Bash commands on a remote UNIX computer or server from your Windows machine. This can be done through a Secure Shell (SSH) client. One such client available for free for Windows computers is PuTTY. See the reference below for information on installing and using PuTTY, using the Windows 10 command-line tool, or installing and using a UNIX/Linux emulator. [How to Install Bash shell command-line tool on Windows 10][win10bashinstall] [Install and Use the Linux Bash Shell on Windows 10][win10bashuse] [win10bashinstall]: https://www.windowscentral.com/how-install-bash-shell-command-line-windows-10 [win10bashuse]: https://www.howtogeek.com/249966/how-to-install-and-use-the-linux-bash-shell-on-windows-10 You should also [install PuTTY][putty] for accessing remote servers [putty]: https://www.putty.org/

« back to top

EDITOR TOP

## Content 1. [ Install a text editor ](#install-a-text-editor) 1. [ Install a text editor ](#install-a-text-editor) --- ### 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++][notepadplus] on Windows * [Sublime Text][sublime] on most other platforms Personal preference : * [PyCharm][pycharm] is a Python programming specific editor with very powerful features. [sublime]: https://www.sublimetext.com/ [notepadplus]: https://notepad-plus-plus.org/ [pycharm]: https://www.jetbrains.com/pycharm/ --- ### Install pandoc [Pandoc][pandoc] can convert documents across formats: `markdown` to `html` or `pdf` etc. On Mac OSX: brew install pandoc On windows visit the [Pandoc][pandoc] website. [pandoc]: http://pandoc.org/ --- ### Online markdown editors * [Dillinger][dillinger] * [StackEdit][stackedit] [dillinger]: http://dillinger.io/ [stackedit]: https://stackedit.io/

« back to 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++][notepadplus] on Windows * [Sublime Text][sublime] on most other platforms Personal preference : * [PyCharm][pycharm] is a Python programming specific editor with very powerful features. [sublime]: https://www.sublimetext.com/ [notepadplus]: https://notepad-plus-plus.org/ [pycharm]: https://www.jetbrains.com/pycharm/ --- ### Install pandoc [Pandoc][pandoc] can convert documents across formats: `markdown` to `html` or `pdf` etc. On Mac OSX: brew install pandoc On windows visit the [Pandoc][pandoc] website. [pandoc]: http://pandoc.org/ --- ### Online markdown editors * [Dillinger][dillinger] * [StackEdit][stackedit] [dillinger]: http://dillinger.io/ [stackedit]: https://stackedit.io/

« back to top

Penn State • generated from bootcamp-central via pyblue