Install PLINK¶
PLINK is a free, open-source whole-genome association analysis toolset. The software is designed flexibly to perform a wide range of basic, large-scale genetic analyses including GWAS.
Step 1: Download PLINK with wget¶
Type these commands into your Ubuntu AWS terminal:
cd /usr/local/bin/
sudo wget https://zzz.bwh.harvard.edu/plink/dist/plink-1.07-x86_64.zip
The first line changes your directory to the "bin". The second line of code downloads the software in the "bin" directory.
Step 2: Unzip¶
Now, uncompress the newly downloaded file:
sudo unzip -o plink-1.07-x86_64.zip
sudo rm plink-1.07-x86_64.zip
cd plink-1.07-x86_64
The first line of code does the uncompressing, the second line of code gets rid of the ".zip" version (you don't need it anymore) and the last line of code takes you into the newly created "plink-1.07-x86_64" directory.
Step 3: Add PLINK to the .bashrc¶
After cd-ing into the "plink-1.07-x86_64" folder, add plink to the .bashrc. By doing so, you are telling the computer that PLINK can be accessed from any directory. Type:
echo export PATH=$PATH:$(pwd) >> ~/.bashrc
source ~/.bashrc
Check to make sure it's installed:
plink -h
The top portion of the help page:
@----------------------------------------------------------@
| PLINK! | v1.07 | 10/Aug/2009 |
|----------------------------------------------------------|
| (C) 2009 Shaun Purcell, GNU General Public License, v2 |
|----------------------------------------------------------|
| For documentation, citation & bug-report instructions: |
| http://pngu.mgh.harvard.edu/purcell/plink/ |
@----------------------------------------------------------@
Please visit the PLINK website for a complete list of options
A few common options are listed here:
plink --file {fileroot} Specify .ped and .map files
--bfile {fileroot} Specify .bed, .fam and .map
--out {fileroot} Specify output root filename
PLINK has now been successfully installed!