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--- guides:available-applications [13.10.2020 10:33]
Juha Kekäläinen created
+++ guides:available-applications [09.06.2021 14:10] (current)
Administrator
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-In the terminal, you can see the list of available software packages by command
+#Available applications on BIC servers
-'modul avail'. A short list of available applications (13.01.2020) below:
-   bamtools/2.5.1                      cufflinks/2.2.1         mothur/1.40.5              r/3.5.3
-   bamutil/1.0.13                      datamash/1.3            openjdk/11.0.2             r/3.6.0
-   bcftools/1.9                        diamond/0.9.21          openmpi/1.10.7-2           r/3.6.1           (D)
-   bedtools2/2.27.1                    fastqc/0.11.7           picard/2.18.3              samtools/1.9
-   blast-plus/2.7.1                    fastx-toolkit/0.0.14    plink/1.07                 sra-toolkit/2.9.2
-   bowtie/1.2                          gcc/8.2.0               plink/1.90b6.12     (D)    star/2.5.1b
-   bowtie/1.2.3                 (D)    hisat2/2.1.0            prinseq-lite/0.20.4        star/2.5.4b
-   bowtie2/2.3.4.1-python-3.7.0        hmmer/3.0               python/2.7.15              star/2.6.1b       (D)
-   breakdancer/master                  htslib/1.9              python/2.7.17              tabix/2013-12-16
-   breakdancer/1.4.5            (D)    jdk/12.0.1              python/3.7.0               trimmomatic/0.36
-   bwa/0.7.17                          matlab/R2018b           python/3.7.3        (D)    vcftools/0.1.14
-   clustalw/2.1                        mono/5.4.1.7            r/3.5.1                    seqan/2.4.0
-   kallisto/0.43.1                     homer/4.9.1             homer/4.10 (D)
-## Lmod Module Environment
+Most of the preinstalled applications on the computing servers are installed as [environment modules](https://lmod.readthedocs.io/en/latest/).
-Applications are managed with the [Lmod Environment Module System](https://lmod.readthedocs.io/en/latest/). Guide for the Lmod can be found [here](https://lmod.readthedocs.io/en/latest/010_user.html)
+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.
-## Quick tutorial:
+**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
-** Available modules **
-    module avail
+** You can search for an package with 'spider' command**
+    module spider homer
-** Load module **
+** 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 **
-    module load python/3.7.3
+** If you wish to Load some specific version number of the application **
+    module load bowtie2/2.3.4.1
-** Unload module **
+** You can also deactivate module**
     module unload bowtie2
-** Save list of loaded modules **
+** Save list of loaded modules for next login**
     module save
-** Restore saved modules **
+** 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.
-## Application location
+** You can quickly go to the application installation path**
-You can quickly go to the application location by writing:
     module load bowtie2
     cd $BOWTIE2_ROOT

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