Differences

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--- plink-software [2015/11/24 13:26] – created joguya
+++ plink-software [2019/12/09 09:10] (current) – aorth
@@ Line 4: / Line 4: @@
 ===== Information =====
-  * Version: 1.9
+  * Version: 2.00-alpha (Nov 28, 2019)
-  * Added: November, 2015
+  * Added: October, 2011
-  * Link: https://www.cog-genomics.org/plink2/
+  * Updated: December, 2019
+  * Link: https://www.cog-genomics.org/plink/2.0/
 ===== Usage =====
@@ Line 13: / Line 14: @@
 <code>$ module avail plink</code>
-Load and run plink:
+Load one version into your environment and run it:
-<code>$ module load plink/1.9
+<code>$ module load plink/2.00-alpha
-$ plink</code>
+$ 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 ======
@@ Line 21: / Line 24: @@
 <code>$ cd /tmp
-$ wget https://www.cog-genomics.org/static/bin/plink151123/plink_linux_x86_64.zip
+$ wget http://s3.amazonaws.com/plink2-assets/plink2_linux_x86_64_20191128.zip
-$ mkdir plink-1.90
+$ sudo mkdir /export/apps/plink/2.00-alpha
-$ cd plink-1.90
+$ sudo cp plink2 /export/apps/plink/2.00-alpha
-$ unzip ../plink_linux_x86_64.zip
+$ rm plink2
-$ sudo mkdir /export/apps/plink/1.9
+$ wget http://s3.amazonaws.com/plink2-assets/plink2_linux_avx2_20191128.zip
-$ sudo cp . /export/apps/plink/1.9
+$ unzip plink2_linux_avx2_20191128.zip
-</code>
+$ 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.