ILRI Research Computing

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====== PLINK ======
PLINK is a whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.

===== Information =====

  * Version: 2.00-alpha (Nov 28, 2019)
  * Added: October, 2011
  * Updated: December, 2019
  * Link: https://www.cog-genomics.org/plink/2.0/

===== Usage =====

See versions of plink which are available:
<code>$ module avail plink</code>

Load one version into your environment and run it:
<code>$ module load plink/2.00-alpha
$ plink2</code>

**Note:** If you are running your job on a newer compute node like compute05 you can run ''plink2-avx2'' instead of ''plink2'' as that server has a newer CPU and can use a more optimized plink.

===== Installation ======
Notes from the sysadmin during installation:

<code>$ cd /tmp
$ wget http://s3.amazonaws.com/plink2-assets/plink2_linux_x86_64_20191128.zip
$ sudo mkdir /export/apps/plink/2.00-alpha
$ sudo cp plink2 /export/apps/plink/2.00-alpha
$ rm plink2
$ wget http://s3.amazonaws.com/plink2-assets/plink2_linux_avx2_20191128.zip
$ unzip plink2_linux_avx2_20191128.zip
$ sudo cp plink2 /export/apps/plink/2.00-alpha/plink2-avx2</code>

The AVX2 build only runs on compute05. The rest of our compute nodes are too old and must use the 64-bit builds.