bedtools on ubuntu 12.0.4

[cmccabe]

 sudo apt-get install zlib1g

 sudo apt-get install zlib1g-dev

 sudo apt-get install bedtools

I do not see a bedtools directory, I didn't get any errors. Thanks.

need to:

make
how to I define the PATH variable?

[dpryan]

If you're doing this on a workstation rather than remotely then you might want to use the "Synaptic package manager" (click on the unity button in the upper left and search for it). You can then simply search for that package and see what was installed and where.

In the case of bedtools, the binaries are in /usr/bin, which is already in your PATH.

For setting your PATH (I'm assuming you didn't change your shell), just add "export PATH=$PATH:/some/new/path" to .bashrc.

[cmccabe]

Is this correct? Thanks.

 "export PATH=$PATH:/home/dnascopev/Desktop/bedtools2-2.20.1"

how do I edit the .bashrc

[dpryan]

Something like that at least should work. You can just execute that from the command line and see if you can then directly execute things in that directory without specifying the full path. BTW, you might want to create a standard directory for programs that only your user has access to (~/bin is common). That way you can just put things in there as you need them and not have to clutter your desktop.

To edit .bashrc, you can use any text editor or just:

echo "export PATH=\$PATH:/home/dnascopev/Desktop/bedtools2-2.20.1" >> ~/.bashrc

The "\" just escapes expansion of the $PATH variable, in case you were wondering.

BTW, you might want to get a book on using Linux/Unix/Mac OS X from the command line. Basic things like this would be covered there.