export JAVA_HOME=/usr/local/java
export PATH=$PATH:$JAVA_HOME/bin
export CLASSPATH=.:$JAVA_HOME/lib/dt.jar:$JAVA_HOME/lib/tools.jar
export JRE_HOME=$JAVA_HOME/jre

(test) root 01:43:30 ~
$ conda activate test
(test) root 01:44:24 ~
$ java -version
java version "1.8.0_291"
Java(TM) SE Runtime Environment (build 1.8.0_291-b10)
Java HotSpot(TM) 64-Bit Server VM (build 25.291-b10, mixed mode)
(test) root 01:44:32 ~
$ conda deactivate
(base) root 01:44:47 ~
$ java -version
java version "1.8.0_291"
Java(TM) SE Runtime Environment (build 1.8.0_291-b10)
Java HotSpot(TM) 64-Bit Server VM (build 25.291-b10, mixed mode)
(base) root 01:44:53 ~

(base) root 01:55:12 ~
$ conda activate test
(test) root 01:55:20 ~
$ cd biosoft/
(test) root 01:55:26 ~/biosoft
$ ls
bget_0.3.2_Linux_64-bit.tar.gz  index.html                  samtools-1.12
download                        javase-jdk8-downloads.html  samtools-1.12.tar.bz2
hisat2-2.2.1                    jre1.8.0_291                Trimmomatic-0.39
hisat2-2.2.1-Linux_x86_64.zip   jre-8u291-linux-x64.tar.gz  Trimmomatic-0.39.zip
(test) root 01:55:39 ~/biosoft
$ cd Trimmomatic-0.39
(test) root 01:56:05 ~/biosoft/Trimmomatic-0.39
$ LS
-bash: LS: command not found
(test) root 01:56:06 ~/biosoft/Trimmomatic-0.39
$ ls
adapters  LICENSE  trimmomatic-0.39.jar
(test) root 01:56:08 ~/biosoft/Trimmomatic-0.39
$ java -jar trimmomatic-0.39.jar
Usage: 
       PE [-version] [-threads <threads>] [-phred33|-phred64] [-trimlog <trimLogFile>] [-summary <statsSummaryFile>] [-quiet] [-validatePairs] [-basein <inputBase> | <inputFile1> <inputFile2>] [-baseout <outputBase> | <outputFile1P> <outputFile1U> <outputFile2P> <outputFile2U>] <trimmer1>...
   or: 
       SE [-version] [-threads <threads>] [-phred33|-phred64] [-trimlog <trimLogFile>] [-summary <statsSummaryFile>] [-quiet] <inputFile> <outputFile> <trimmer1>...
   or: 
       -version
(test) root 01:57:18 ~/biosoft/Trimmomatic-0.39

(test) root 01:59:27 ~
$ java -jar /root/biosoft/Trimmomatic-0.39/trimmomatic-0.39.jar --help
Usage: 
       PE [-version] [-threads <threads>] [-phred33|-phred64] [-trimlog <trimLogFile>] [-summary <statsSummaryFile>] [-quiet] [-validatePairs] [-basein <inputBase> | <inputFile1> <inputFile2>] [-baseout <outputBase> | <outputFile1P> <outputFile1U> <outputFile2P> <outputFile2U>] <trimmer1>...
   or: 
       SE [-version] [-threads <threads>] [-phred33|-phred64] [-trimlog <trimLogFile>] [-summary <statsSummaryFile>] [-quiet] <inputFile> <outputFile> <trimmer1>...
   or: 
       -version
(test) root 02:00:17 ~

(test) root 02:00:17 ~
$ trimmomatic=$HOME/biosoft/Trimmomatic-0.39/trimmomatic-0.39.jar
(test) root 02:02:53 ~
$ echo $HOME
/root
(test) root 02:03:16 ~
$ echo $trimmomatic
/root/biosoft/Trimmomatic-0.39/trimmomatic-0.39.jar
(test) root 02:03:44 ~
$ java -jar $trimmomatic 
Usage: 
       PE [-version] [-threads <threads>] [-phred33|-phred64] [-trimlog <trimLogFile>] [-summary <statsSummaryFile>] [-quiet] [-validatePairs] [-basein <inputBase> | <inputFile1> <inputFile2>] [-baseout <outputBase> | <outputFile1P> <outputFile1U> <outputFile2P> <outputFile2U>] <trimmer1>...
   or: 
       SE [-version] [-threads <threads>] [-phred33|-phred64] [-trimlog <trimLogFile>] [-summary <statsSummaryFile>] [-quiet] <inputFile> <outputFile> <trimmer1>...
   or: 
       -version
(test) root 02:04:21 ~
$ java -jar $trimmomatic --help
Usage: 
       PE [-version] [-threads <threads>] [-phred33|-phred64] [-trimlog <trimLogFile>] [-summary <statsSummaryFile>] [-quiet] [-validatePairs] [-basein <inputBase> | <inputFile1> <inputFile2>] [-baseout <outputBase> | <outputFile1P> <outputFile1U> <outputFile2P> <outputFile2U>] <trimmer1>...
   or: 
       SE [-version] [-threads <threads>] [-phred33|-phred64] [-trimlog <trimLogFile>] [-summary <statsSummaryFile>] [-quiet] <inputFile> <outputFile> <trimmer1>...
   or: 
       -version
(test) root 02:04:29 ~