Download Utilities

After locating the MethPipe files that we will need later in the analysis work flow, we first download the executables and place them into the Tools folder. We will use them for data file manipulation. We use the chmod command to make the programs executable.

cd ~/Tools
wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedGraphToBigWig
wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedToBigBed
chmod 755 bedGraphToBigWig bedToBigBed

Now check if you can access bedtools utilities by trying one of its programs, such as sortBed -h

For reader who do not have an account on the ALPS server, please download the bedtools utilities (latest version is 2.22.0 at the time of writing) and compile it with make. The compiled executables will be located in the bedtools-2.22.0/bin folder. You may set up the PATH environment variable so that you can use any of the bedtools programs by calling its name without having to write the full file path.

cd ~/Tools
wget -O bedtools-2.22.0.tar.gz 'https://github.com/arq5x/bedtools2/releases/download/v2.22.0/bedtools-2.22.0.tar.gz'
tar zxf bedtools-2.22.0.tar.gz

cd bedtools2
make