Differences

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--- trimmomatic-software [2015/09/25 08:22] – created joguya
+++ trimmomatic-software [2021/09/05 11:10] (current) – aorth
@@ Line 4: / Line 4: @@
 ===== Information =====
-  * Version: 0.33
+  * Version: 0.39
   * Added: September, 2015
-  * Link: http://www.usadellab.org/cms/?page=trimmomatic
+  * Updated: September, 2021
+  * Link: https://github.com/usadellab/Trimmomatic
 ===== Usage =====
@@ Line 13: / Line 14: @@
 <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>
@@ Line 20: / Line 21: @@
 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)
-java -jar $PREFIX/trimmomatic-0.33.jar $*
+java -jar $PREFIX/trimmomatic-0.39.jar $*</code>
-</code>