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trimmomatic-software [2015/09/25 08:22]
joguya created
trimmomatic-software [2021/09/05 11:10] (current)
aorth
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 ===== Information ===== ===== Information =====
  
-  * Version: 0.33+  * Version: 0.39
   * Added: September, 2015   * Added: September, 2015
-  * Link: http://www.usadellab.org/cms/?page=trimmomatic+  * Updated: September, 2021 
 +  * Link: https://github.com/usadellab/Trimmomatic
  
 ===== Usage ===== ===== Usage =====
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 <code>$ module avail trimmomatic</code> <code>$ module avail trimmomatic</code>
  
-Load and run trimmomatic+Load one version into your environment and run it
-<code>$ module load trimmomatic/0.33+<code>$ module load trimmomatic/0.39
 $ trimmomatic</code> $ trimmomatic</code>
  
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 Notes from the sysadmin during installation: Notes from the sysadmin during installation:
  
-<code>$ cd /tmp/ +<code>$ cd /tmp 
-$ wget http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.33.zip +$ wget http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.39.zip 
-cd Trimmomatic-0.33 +unzip Trimmomatic-0.39.zip 
-$ sudo mkdir -p /export/apps/trimmomatic/0.33 +$ sudo mkdir -p /export/apps/trimmomatic/0.39 
-$ sudo cp -rv . /export/apps/trimmomatic/0.33/ +$ sudo cp -r Trimmomatic-0.39/* /export/apps/trimmomatic/0.39</code>
-</code>+
  
-I created a wrapper shell script named ''trimmomatic'' to run Trimmomatic, otherwise, you'll have to specify a path to trimmomatic-0.33.jar—''java -jar <path to trimmomatic.jar> ...''—which is unfriendly. ''/export/apps/trimmomatic/0.33/trimmomatic'':<code> +Trimmomatic is distributed as a jar file and is not easy for users to run. I created a wrapper shell script named ''trimmomatic'': 
-#!/usr/bin/env bash+ 
 +<code>#!/usr/bin/env bash
  
 readonly PREFIX=$(dirname $0) readonly PREFIX=$(dirname $0)
-java -jar $PREFIX/trimmomatic-0.33.jar $* +java -jar $PREFIX/trimmomatic-0.39.jar $*</code>
-</code>+
trimmomatic-software.1443169357.txt.gz · Last modified: 2015/09/25 08:22 by joguya