#Available applications on BIC servers

Most of the preinstalled applications on the computing servers are installed as [environment modules](https://lmod.readthedocs.io/en/latest/).

To use application you first must activate it. This will modify the [environment variables](https://en.wikipedia.org/wiki/Environment_variable) 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