added pck manager info

Author: HadrienG

unix/running.md

@@ -0,0 +1,90 @@
+# Introduction to Unix (continued)
+
+In this part of the tutorial, we'll learn how to install programs in a Unix system
+
+## Using a package manager
+
+This is the most straight-forward way, and the way used by most of the people using unix at home,
+or administrating their own machine.
+
+This course is aimed at giving you a working knowledge of linux for bioinformatics, and in that setting, you will rarely, if ever, be the administrator of your own machine. The methods below are here as an information
+
+### On Ubuntu and Debian: Apt
+
+To install a software:
+
+`apt-get install name_of_the_software`
+
+to uninstall:
+
+`apt-get remove name_of_the_software`
+
+to update all installed softwares:
+
+```
+apt-get update
+apt-get upgrade
+```
+
+### On Fedora, CentOS and RedHat: yum
+
+To install a software:
+
+`yum install name_of_the_software`
+
+to uninstall:
+
+`yum remove name_of_the_software`
+
+to update:
+
+`yum update`
+
+### MacOS: brew
+
+Although there are no official package managers on MacOS, two popular, community-driven alternatives exist: macports and brew.
+
+Brew is particularly pupular within the bioinformatics community, and allows easy installation of many bioinformatics softwares on MacOS
+
+To install brew on your mac:
+
+`/usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"`
+
+To install a software:
+
+`brew install name_of_the_software`
+
+To uninstall:
+
+`brew uninstall name_of_the_software`
+
+To update all brew-installed softwares:
+
+```
+brew update
+brew upgrade
+```
+
+More info on [brew.sh](http://brew.sh) and [brew.sh/homebrew-science/](http://brew.sh/homebrew-science/)
+
+## Downloading binaries
+
+In a university setting, you will rarely by administrator of your own machine. This is a very good thing for one reason: it's harder for you to break something!
+
+The downside is that it makes installing softwares more complicated. We'll start wit simply downloading the software and executing it, then we'll learn how to obtain packages from source code.
+
+for example, we'll install the blast binaries:
+
+First, download the archive:
+`wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.6.0+-x64-linux.tar.gz`
+
+then unpack it and go to the newly created directory
+
+```
+tar xzf ncbi-blast-2.6.0+-x64-linux.tar.gz
+cd ncbi-blast-2.6.0+
+```
+
+you should have a `bin` directory, go inside and look at the files. You have a bunch of executable files.
+
+### Execute a file