I am installing cufflinks on my Mac OS X, and here is the instruction:
http://cufflinks.cbcb.umd.edu/tutorial.html
Under Installing the SAM tools I follow the instructions below
I've done the fist 7 steps, but I am not sure how to proceed with the last step (#8): should I use the command:
sudo cp -a samtools-0.1.18 /usr/local/
or into some other directories? What does the PATH in step 8 indicate? Thanks!
To answer your question I will go over some basic linux knowledge that has helped me understand binaries and their locations.
In linux, you can run a binary by typing in a complete path to the binary and the binary will run. For example, if I have a binary named foo
in /usr/local/bin
, I would run the command /usr/local/bin/foo
and the foo
binary would be run.
The purpose of the PATH is a shortcut so that you don't need to type in the complete path to the binary, just the name of the binary. PATH is a variable that contains all of the directories that have binaries that you want to have the shortcut apply to. So, referring to the previous example, if /usr/local/bin
is in my PATH variable, then I could just run foo
.
So, to answer your question, you can tell which directories that are in your PATH by running the command echo $PATH
and if one of the directories is where your samtools binaries are, your good!! If not, you can move your samtools binaries to one of those directories so that you don't have to put the full path everytime you want to run the binaries.