#How to add packages to mac os el capitan installer install#

With a clean install of El Capitan, SIP has not caused any issues for me. SIP locks down all system files even for users with root access. In El Capitan, Apple introduced a new security feature called System Integrity Protection (SIP). Upgrading from Yosemite and a note on SIP You’re also ready to use Homebrew, pip, and R’s package manager to add more tools at your discretion. That’s it! You’re now ready to get started with Python and R. Again, you can install Atom via brew: brew cask install atom Wrap-up Unlike TextWrangler (and Sublime Text which also has a large following), Atom is both free and open-source. I now use Atom in place of both TextWrangler, which I used as a general purpose text editor, and P圜harm, which I used for Python development. Install Atom for general text-editing and scriptingĪtom is an excellent new text editor from the team behind Github. You can install MacTex by running: brew cask install mactex 9.

#How to add packages to mac os el capitan installer full#

Unless you’re experienced with MacTeX, go with the full MacTeX installation rather than BasicTeX.

#How to add packages to mac os el capitan installer full version#

The installer for the full version of MacTeX is giant (~3GB), but worth it if you plan to share your work as a PDF. To export Rmarkdown documents as PDFs, which I often do to share analyses with colleagues, RStudio requires MacTeX. You can download the installer from RStudio’s website. I recommend it to anyone who writes any R code. I normally avoid integrated development environments because they tend to be overkill for my biocomputing needs, but RStudio is relatively lightweight. You will probably also want to install a few of Hadley Wickham’s packages: R # Launch R > install.packages ( 'tidyverse' ) 6. Run the following commands to install R: brew tap brewsci/science Installing Jupyter via pip will install IPython Notebook: pip install jupyter 5. IPython Notebook, another popular biocomputing tool, is now a part of the Jupyter Project. We’ll install that next, again using pip: pip install biopython One of the most commonly used biocomputing Python libraries is Biopython. Pip install pandas # Dataframes in Python! Pip install scipy # Other scientific computing tools Use pip to install a few Python libraries: pip install numpy # Vectors and matrices in Python Homebrew’s version of Python comes with pip, a package manager specifically designed for Python libraries. Both Python 2 and Python 3 can be installed concurrently. If you would like to install Python 3 instead, replace python in the above command with python3. Let’s install a separate, newer version of Python 2.7.x: brew install python Install PythonĪgain, like git, the default Python installation in OS X also tends to be outdated. Rather than overwrite the system git installation, we’ll install a new version of git via Homebrew: brew install git 4. Xcode tends to come with older versions of git and Apple is slow to keep git up-to-date. Git is a version control system commonly used with Github. Install git for version controlĪfter Homebrew has been installed, installing other software is relatively simple. To install Homebrew, run this command and follow the prompts: ruby -e ' $(curl -fsSL ) ' 3. The rest of this guide will assume that you have Homebrew installed, though you could just as easily use MacPorts to install git, Python, and R. I prefer Homebrew to MacPorts because of a variety of issues that I’ve had with MacPorts. Install Homebrew for managing software packages Install Xcode Command Line Tools with the following command in the Terminal: xcode-select -installįollow the prompts and accept the license agreement. The Xcode Command Line Tools are provided by Apple and contain the necessary tools for compiling code and installing other software. Many of the following steps for El Capitan were derived from her post. If you are interested in configuring Yosemite for biocomputing instead, see this post by Stephanie Spielman. This guide describes the steps I took to configure El Capitan for biocomputing. To cleanly rid my laptop of MacPorts, I started with a fresh copy of El Capitan.

I did this for several reasons, but mostly because I was thoroughly frustrated with MacPorts and wanted to switch to Homebrew (more on that later).

#How to add packages to mac os el capitan installer mac os x#

I recently wiped my Macbook Pro and reinstalled Mac OS X El Capitan. So feel free to use this guide to set up macOS Sierra for biocomputing.

#How to add packages to mac os el capitan installer update#

Update (3/26/17): After six months of using macOS Sierra, I can state confidently that all instructions discussed below hold true for both El Capitan and Sierra. Update (3/28/18): This post has been updated to reflect changes in how scientific software is distributed in Homebrew.