Most of the preinstalled applications on the computing servers are installed as environment modules.

To use application you first must activate it. This will modify the environment variables so that the application and all its dependencies are found.

To find the available modules you will need to use the following command in terminal

module avail

This will give you an list of all the available modules. For example list of available applications (13.01.2020) below:

 
 ambertools/20      eagle/2.4.1                  nextflow/19.10          snptest/2.5.2
 bcl2fastq2/2.20    freesurfer/7.1               nf-core/1.8             snptest/2.5.4-beta3
 chilin/2.0         igv/2.8.0                    sentieon/201911         texlive/2019
 cuda/10.1          minimac4/1.0.2               shapeit/2.17            vcftools/0.1.14
 bamtools/2.5.1     fastqc/0.11.7                openmpi/1.10.7-2        r/3.5.3
 bamutil/1.0.13     fastx-toolkit/0.0.14         openmpi/3.1.4           r/3.6.1
 bcftools/1.9       freebayes/1.1.0              picard/2.18.3           r/4.0.0
 bedtools2/2.27.1   hisat2/2.1.0                 plink/1.07              samtools/1.9
 bowtie/1.2.3       homer/4.10                   plink/1.90b6.12         sra-toolkit/2.9.2
 bowtie2/2.3.4.1    htslib/1.9                   plink/2.00a2.3LM        star/2.6.1b
 bwa/0.7.17         matlab/R2015b                python/2.7.15           stringtie/1.3.4a
 clustalw/2.1       matlab/R2018b                python/2.7.17           tabix/2013-12-16
 cufflinks/2.2.1    openjdk/1.8.0_202-b08        python/3.7.0            trimmomatic/0.36
 diamond/0.9.21     openjdk/11.0.2               python/3.7.3

To activate the application you can use the following command

module load bowtie2

Note that you can activate multiple applications but you cannot activate multiple versions of the same application.

If you wish to Load some specific version number

module load bowtie2/2.3.4.1

You can also deactivate module

module unload bowtie2

Save list of loaded modules for next login

module save

Restore list of saved modules

module restore

You can quickly go to the application location

module load bowtie2
cd $BOWTIE2_ROOT