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 of the user so that the application and all its dependencies are available for usage.

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 on SAMPO cluster (09.06.2021):

 
 ambertools/20      freesurfer/7.1          nextflow/19.10               sentieon/201911      texlive/2019
 bcl2fastq2/2.20    igv/2.8.0               nextflow/20.12.0-edge        sentieon/202010      sra-toolkit/2.9.2
 chilin/2.0         macs/2.2.7.1            nextflow/21.04.1             shapeit/2.17         star/2.6.1b
 cuda/10.1          minimac4/1.0.2          nf-core/1.8                  snptest/2.5.2        vcftools/0.1.14
 eagle/2.4.1        msdial/4.60             pyega3/3.4.1                 snptest/2.5.4-beta3  stringtie/1.3.4a 
 bamtools/2.5.1     clustalw/2.1            matlab/R2015b                python/2.7.15        tabix/2013-12-16
 bamutil/1.0.13     cufflinks/2.2.1         matlab/R2018b                python/2.7.17        trimmomatic/0.36
 bcftools/1.9       diamond/0.9.21          openjdk/1.8.0_202-b08        python/3.7.0         
 bcftools/1.10.2    fastqc/0.11.7           openjdk/11.0.2               python/3.7.3         
 bedops/2.4.39      fastx-toolkit/0.0.14    openmpi/1.10.7-2             r/3.5.3              
 bedtools2/2.27.1   freebayes/1.1.0         openmpi/3.1.4                r/3.6.1              
 bedtools2/2.29.2   gcc/8.2.0               picard/2.18.3                r/4.0.0          
 bowtie/1.2.3       hisat2/2.1.0            plink/1.07                   samtools/1.9
 bowtie2/2.3.4.1    homer/4.10              plink/1.90b6.12              samtools/1.10    
 bwa/0.7.17         htslib/1.9              plink/2.00a2.3LM             seqtk/1.3

You can search for an package with 'spider' command

module spider homer

To activate the application you can use the following command

module load bowtie2

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

If you wish to Load some specific version number of the application

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

Note: If you add this line to your $HOME/.bashrc file then the modules are automatically loaded on login.

You can quickly go to the application installation path

module load bowtie2
cd $BOWTIE2_ROOT