# 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.

```bash
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](https://github.com/arq5x/bedtools2) (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.

```bash
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
```


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