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-#Available applications on BIC servers 
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-Most of the preinstalled applications on the computing servers are installed as [environment modules](https://lmod.readthedocs.io/en/latest/). 
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-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. 
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-**To find the available modules you will need to use the following command in terminal** 
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-    module avail 
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-This will give you an list of all the available modules. 
-For example list of available applications on SAMPO cluster (09.06.2021): 
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-   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 
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-** You can search for an package with 'spider' command** 
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-    module spider homer 
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-** To activate the application you can use the following command** 
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-    module load bowtie2 
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-Note: You can activate multiple applications **but** you cannot activate multiple versions of the same application. 
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-** If you wish to Load some specific version number of the application ** 
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-    module load bowtie2/2.3.4.1 
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-** You can also deactivate module** 
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-    module unload bowtie2 
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-** Save list of loaded modules for next login** 
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-    module save 
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-** Restore list of saved modules** 
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-    module restore 
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-Note: If you add this line to your $HOME/.bashrc file then the modules are automatically loaded on login. 
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-** You can quickly go to the application installation path** 
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-    module load bowtie2 
-    cd $BOWTIE2_ROOT 
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guides/available-applications.1741785154.txt.gz · Last modified: 12.03.2025 15:12 by Administrator

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