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guides:available-applications [13.10.2020 10:33]
Juha Kekäläinen created 		guides:available-applications [11.12.2020 13:30]
Juha Kekäläinen
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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 (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
  
-** Available modules **+** You can search for an package with 'spider' command**
  
-    module avail+    module spider homer
  
- +** To activate the application you can use the following command**
-** Load module **+
  
     module load bowtie2     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     module unload bowtie2
  
  
-** Save list of loaded modules **+** Save list of loaded modules for next login**
  
     module save     module save
  
  
-** Restore saved modules **+** Restore list of saved modules**
  
     module restore     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     module load bowtie2
     cd $BOWTIE2_ROOT     cd $BOWTIE2_ROOT
 +    
 + 
  
guides/available-applications.txt · Last modified: 09.06.2021 14:10 by Administrator

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