Homebrew is a package manager for OS X that it much easier to install Linux/Unix packages. Go to the Homebrew webpage and follow the install instructions there. After Homebrew is. Hash -d brew brew bundle install -file /path/to/Brewfile` Optionally run brew analytics off to turn of the tracking/analytics gathering done be Homebrew ( ) PS: Some formulae don't seem to work on ARM yet. Once you’ve set up Homebrew, just run brew install wget in the Terminal. Windows users don’t have easy access to wget in the traditional Command Prompt, though Cygwin provides wget and other GNU utilities, and Windows 10’s Ubuntu’s Bash shell also comes with wget. Brew tap emqx/emqx 2. Install brew install emqx 3. Run emqx start 1. Download currentPackagesArchitecture SHA256 wget downloadLink 2. A good starting point for contributing is running brew audit -strict with some of the packages you use (e.g. Brew audit -strict wget if you use wget) and then read through the warnings, try to fix them until brew audit -strict shows no results and submit a pull request.
This is the second offering of BIS180L as a remote class; we found last year that it works very well in remote format. This class was already designed as a computer only class so there are no significant change in content due to remote delivery.
Lectures will be pre-recorded and available by 9AM the day before the lecture/lab time. You will need to watch them in advance and answer embedded quiz questions via playposit. Due date for the quiz is 9AM the day of lecture. This give me and the TA time to review questions before class.
During lecture/lab-time we will meet via Zoom. We will devote the beginning of each class / lab to questions on the lecture material. I will then split you into groups of two or three in zoom breakout rooms to work on the lab material. John (TA) and I will drop into your breakout rooms when you have questions. We will reconvene as a full Zoom group occasionally through the session.
I expect you to be available during the class / lab periods to participate in the Zoom sessions. If you are unable to do this due to the disruptions caused by COVID-19 and remote instruction, or if you are in a different time zone, please email me or message me through Canvas.
You will need a laptop for this course (Chromebook OK).24 Mar 2021
We will use Vince Buffalo’s excellent book Bioinformatics Data Skills.
This book is available online for free through the UC Davis Library (on campus or VPN connection required). UC is licensed for simultaneous access by 28 people. If that doesn’t work for you, you can buy it direct from the publisher or from amazon. As of this posting Amazon is cheaper and has used copies as well.
Additionally we will use Hadley Wickham’s also excellent book R for Data Science which is available online for free. If you would like a physical copy, here is the amazon link05 May 2020
If you want to try doing the labs directly on your Mac instead of on AWS here is how you can. This document may have errors; please let me know and I can help (and update the document)
Install the following packages by clicking on the link and following the instructions on the web page:
- The atom editor
- The R statistical programming language
- The R IDE Rstudio
- The sequence alignment viewer jalview # maybe not used
- The network viewer cytoscape # maybe not used
Open up atom, click on File > Preferences, and then install the following atom packages. Not all of these are needed for the BIS180L but they are good to have
In Atom go to preferences and search for the ‘whitespace’ package. Disable it.
XCode command line tools
First you need to install Xcode, Apple’s development software that includes compilers necessary for installing packages from source.
We only need the Xcode command-line tools, you can install them by entering the command below in the Unix terminal:
(If you prefer, you can install the whole GUI instead but it takes up a lot of space and you will probably never use it.)
Homebrew is a package manager for OS X that it much easier to install Linux/Unix packages.
Go to the Homebrew webpage and follow the install instructions there.
After Homebrew is installed, then from a terminal window:
install the following packages through homebrew
Open RStudio and then
Still within R, install Bioconductor
For auto_barcode to work, the following must be installed (From the Unix command line):
add class data
IMPORTANT: I AM GIVING THIS A DIFFERENT PATH THAN USED IN THE LAB TO REDUCE THE CHANCE OF YOU OVERWRITING FILES ON YOUR COMPUTER. On the website it this is
~/data but here it is
~/bis180l/data. ``~/bis180l/data` will be overwritten so make sure that nothing critical is there.
Still need to deal with trimmomatic and auto_barcode, but the instructions in the labs should more or less work.
I can’t get this to work, you will need to use your instance for this one.
Manage different versions of homebrew packages
Manage multiple versions of your Homebrew packages with ease!Homebrew makes this difficult as a design decision, but sometimes old packagesneed to be installed and we need a way to do so easily.
Or just with pip:
Switch to a specific version:
Installing from taps:
When no bottle is found for taps it will proceed with searching thelocal tap repository for the correct version and installing from the bottledefined in the formula if it exists, otherwise from source.
This is very slow for the main homebrew repository so this behaviour is disabledwhen a bottle for a homebrew-core package cannot be found. You can supplythe option
brewv switch --slow ... to perform this search.
Proper SHA256 verification is not done when downloading bottles from themain bottle repository. This is because to get the expected SHAs would mean searchingthe huge homebrew-core repository.
While homebrew bottles exist for most operatingsystems, if the bottle is not found then parsing old formulas fails quite oftensince Homebrew updates their code frequently.
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