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--- guides:available-applications [11.12.2020 13:30]
Juha Kekäläinen
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-#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 (13.01.2020):
-   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
-** 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

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