Wget Brew

$ brew install wget Homebrew ติดตั้งแพคเกจต่าง ๆ ไปที่ไดเรคทอรี่ที่แยกไว้ต่างหาก จากนั้นทำการ symlinks ไฟล์เหล่านั้นไปที่ /usr/local. My wget stop working. When I tried to install by typing. Brew install wget -with-libressl I got the following warning. Warning: wget-1.19.1 already installed, it's just not linked. Then tried to unsintall by typing. Brew uninstall wget -with-libressl Then I reinstalled by typing. Brew install wget -with-libressl Finally I got it.

There are two fantastic tools to install on you new Mac: After you install iTerm2, it’s time to install Homebrew!

Homebrew is a package manager – think apt-get for OS X. It is trivial to install and instantly gives you access to thousands of open source tools and utilities. According to the creators of Homebrew, “Homebrew installs the stuff you need that Apple didn’t.”

Visit http://brew.sh right now to get started!

Speedtest® CLI Internet connection measurement for developers. Speedtest CLI brings the trusted technology and global server network behind Speedtest to the command line. In addition, Wget also supports HSTS (HTTP Strict Transport Security). If Wget is compiled without SSL support, none of these options are available. Likewise, which is better curl or wget? The main differences are: wget 's major strong side compared to curl is its ability to download recursively. Brew search name. To download and install that package: brew install name. To remove that package from your system later: brew remove name. For more details on using these commands, read the Homebrew Cask Usage guide or the Homebrew brew command manual on their official websites. Not every graphical application or Unix utility you’re looking.

Top 10 (or more) most useful Homebrew apps to get you started. (Paste this list into your terminal once you get Homebrew installed.)

Wget Install Brew Osx

Screenshot showing Homebrew installing mtr on Mac OS X.

(mtr is a fun and useful ICMP tool which combines ping and traceroute into a realtime display of packet loss across all the path entries returned by traceroute.)

Enjoy!

Dear Students,

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).

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 link

What Brew

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)

web downloads

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

Atom packages

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

• Sublime-Style_Column-Selection
• language-markdown
• git-plus
• markdown-pdf
• line-ending-converter

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

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:

upgrade homebrew

install the following packages through homebrew

R packages

Open RStudio and then

Still within R, install Bioconductor

Wget Os X

perl modules

For auto_barcode to work, the following must be installed (From the Unix command line):

tophat

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.

Other

Still need to deal with trimmomatic and auto_barcode, but the instructions in the labs should more or less work.

Wget Brave Browser

fastStructure

I can’t get this to work, you will need to use your instance for this one.

Beer Brewing Software