Running jar file

[mahmood]

May I ask what is the correct syntax for running a jar file? I saw that the following command should be fine.

Code: Select all

[root@rocks7 Trimmomatic-0.36]# /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.151-1.b12.el7_4.x86_64/jre/bin/java -jar trimmomatic-0.36.jar
Usage:
       PE [-version] [-threads <threads>] [-phred33|-phred64] [-trimlog <trimLogFile>] [-quiet] [-validatePairs] [-basein <inputBase> | <inputFile1> <inputFile2>] [-baseout <outputBase> | <outputFile1P> <outputFile1U> <outputFile2P> <outputFile2U>] <trimmer1>...
   or:
       SE [-version] [-threads <threads>] [-phred33|-phred64] [-trimlog <trimLogFile>] [-quiet] <inputFile> <outputFile> <trimmer1>...
   or:
       -version
[root@rocks7 Trimmomatic-0.36]#

[avij]

The syntax is OK, the error comes from the .jar you are trying to run. Apparently it needs some parameters of its own. Check the trimmomatic documentation (wherever that is).