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tassel-software [2015/09/22 14:02] – [Installation] aorthtassel-software [2024/10/22 12:53] (current) – aorth
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 ===== Information ===== ===== Information =====
-  * Version: 4.0 +  * Version: 5.2.94 
-  * Added: August, 2014 +  * Added: November, 2021 
-  * Link: http://www.maizegenetics.net/tassel+  * Updated: October, 2024 
 +  * Link: https://www.maizegenetics.net/tassel
  
 ===== Usage ===== ===== Usage =====
-See which versions of tassel are  available:+See which versions are available:
  
 <code>$ module avail tassel</code> <code>$ module avail tassel</code>
  
-Load one version into your shell's environment:+Load one version into your shell's environment and run it:
  
-<code>$ module load tassel/4.0</code>+<code>$ module load tassel/5.2.94 
 +$ run_pipeline.pl</code>
  
-==== Memory Usage/Settings ==== +**Note:** Tassel uses a default memory of ''-Xms512m -Xmx1536m'', so you will probably want to increase that so it doesn't crash, for example: ''run_pipeline.pl -Xms512m -Xmx4096m''
-  * Tassel uses java with a default memory setting of: -Xms512m -Xmx1536m +
-  * So you have to increase the maximum memory(-Xmx) to atleast 4GB otherwise tassel would run out of memory really fast +
-  * Use the following options to set the maximum memory size to 4GB:<code>-Xms512m -Xmx4096m</code> +
-  * For example:<code>run_pipeline.pl -Xms512m -Xmx4096m</code> +
- +
-==== Installation ===== +
-Notes from the sysadmin during installation: +
- +
-<code>$ git clone git://git.code.sf.net/p/tassel/tassel3-standalone tassel3 +
-$ cd tassel3/ +
-$ git checkout V3.0.165 +
-$ sudo mkdir -p /export/apps/tassel/3.0.165 +
-$ sudo cp -rv * /export/apps/tassel/3.0.165</code>+
  
 ===== Sample Script ===== ===== Sample Script =====
-Sample script for running via SLURM:+Sample sbatch script for running via SLURM, //tassel.sbatch//:
  
-<file>#!/bin/env bash+<file>#!/usr/bin/env bash
  
 #SBATCH -p batch #SBATCH -p batch
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 #SBATCH -n 10 #SBATCH -n 10
  
-current_date=$(date +%b_%d)+current_date=$(date +%Y-%m-%d)
  
 DATADIR="/home/monyango/data/cullicoides_br/$current_date" DATADIR="/home/monyango/data/cullicoides_br/$current_date"
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 # step 7: output hapmap file # step 7: output hapmap file
 run_pipeline.pl -Xmx4096m -fork1 -UMapInfoToHapMapPlugin -w ${DATADIR}/UNEAK -mnMAF 0.05 -mxMAF 0.5  -mnC 0 -mxC 1 -endplugin -runfork1</file> run_pipeline.pl -Xmx4096m -fork1 -UMapInfoToHapMapPlugin -w ${DATADIR}/UNEAK -mnMAF 0.05 -mxMAF 0.5  -mnC 0 -mxC 1 -endplugin -runfork1</file>
 +
 +==== Installation =====
 +Notes from the sysadmin during installation:
 +
 +<code>$ git clone https://bitbucket.org/tasseladmin/tassel-5-standalone.git -b V5.2.94
 +$ cd tassel-5-standalone
 +$ sudo mkdir -p /export/apps/tassel/5.2.94
 +$ sudo cp -rv * /export/apps/tassel/5.2.94</code>
tassel-software.1442930520.txt.gz · Last modified: by aorth