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infrastructure:solu [19.06.2019 10:50]
Juha Kekäläinen 		infrastructure:solu [13.10.2020 12:14] (current)
Juha Kekäläinen
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 # solu.uef.fi # solu.uef.fi
  
-## Introduction +Solu (finnish word for Cell) computing server is meant for an interactive computing workloads. In addition to the traditional SSH terminal access the server provides graphical desktop environment that can be used with the [Remote Desktop Connection Protocol](https://en.wikipedia.org/wiki/Remote_Desktop_Protocol).
- +
-Solu (finnish word for Cell) Computing Server is for the interactive computing workloads. Additionally to the traditional SSH access the server provides graphical desktop environment that can be used with the [Remote Desktop Connection Protocol](https://en.wikipedia.org/wiki/Remote_Desktop_Protocol).+
  
 Server address: **solu.uef.fi** Server address: **solu.uef.fi**
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 ## Storage ## Storage
 +
 Server is connected to the storage space provided by the [UEF IT Services for Research](https://www.uef.fi/web/tipa/tipa). More information can be found from the [[infrastructure:guides:storage-space|dedicated page]]. Server is connected to the storage space provided by the [UEF IT Services for Research](https://www.uef.fi/web/tipa/tipa). More information can be found from the [[infrastructure:guides:storage-space|dedicated page]].
  
-## Applications 
  
-System provides various graphical and terminal applications for the researchers.+## Available reference data set
  
-Additionally to browser, office-suite and text editors the following graphical applications are available:+All the available reference data sets are provided as-is. They are unmodified copies of the original files. 
  
-^Graphical Applications ^Version^ +## iGenomes
-|MATLAB                             |   R2018b            | +
-|RStudio                            |   3.5.1             | +
-|RStudio                            |   3.6.0             | +
-|RStudio-Server                     |   3.6.0             | +
-|IGV                                |   2.5.2             |+
  
-^Other Applications ^Version ^Address^ +URL: [[https://support.illumina.com/sequencing/sequencing_software/igenome.html]]
-|[Rstudio-Server](https://www.rstudio.com/products/rstudio/)|   3.6.0|https://solu.uef.fi/rstudio| +
-|[Singularity Container](https://www.sylabs.io/singularity/)|   3.2.1|             +
  
 +Following reference genomes can be found from the ** /apps/genomes/iGenomes ** folder.
  
 +^Home sapiens ^Version^
 +|GRCh37                             |   Ensembl       |
 +|GRCh38                             |   NCBI          |
 +|GRCh38Decoy                        |   NCBI          |
 +|hg19                               |   UCSC          |
 +|hg39                               |   UCSC          |
  
-For the terminal applications use the 'module avail' command. Short list of available applications (19.06.2019) below: +^Mus musculus ^Version^ 
-    +|mm9                              |   UCSC       | 
-   homer/4.9.1                         kallisto/0.43.1 +|mm10                             |   UCSC       |
-   bamtools/2.5.1                      cufflinks/2.2.1               matlab/R2018b              r/3.6.0          (L,D) +
-   bamutil/1.0.13                      datamash/1.3                  mono/5.4.1.7               samtools/1.9 +
-   bcftools/1.9                        diamond/0.9.21                openmpi/1.10.7-2           star/2.5.1b +
-   bedtools2/2.27.1                    fastqc/0.11.7                 picard/2.18.3              star/2.5.4b +
-   bowtie/1.2                          fastx-toolkit/0.0.14          plink/1.07                 star/2.6.1b      (D) +
-   bowtie2/2.3.4.1-python-3.7.0        gcc/8.2.0                     prinseq-lite/0.20.4        tabix/2013-12-16 +
-   breakdancer/master                  hisat2/2.1.0                  python/2.7.15       (L)    trimmomatic/0.36 +
-   breakdancer/1.4.5            (D)    htslib/1.9                    python/3.7.0               vcftools/0.1.14 +
-   bwa/0.7.17                          jdk/11.0.3                    python/3.7.3        (D) +
-   clustalw/2.1                        jdk/12.0.1           (L,D)    r/3.5.1+
  
-## Lmod Module Environment+^Rattus norvegicus ^Version^ 
 +|rn4                              |   UCSC       |
  
-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)+## gnomAD
  
-## Quick tutorial:+URL: [[https://gnomad.broadinstitute.org/downloads]]
  
 +Following variants can be found from the ** /research/groups/bioinformaticians/gnomAD-hg19-r2.1.1 ** folder.
  
 +^Data set ^Version^
 +|Exome variants (.vcf.bgz, tbi)          |   gnomAD 2.1.1 / hg19       |
 +|Exome calling regions (.interval list)  |   gnomAD 2.1.1 / hg19       |
 +|Genome variants (.vcf.bgz, tbi)         |   gnomAD 2.1.1 / hg19       |
 +|Genome calling regions (.interval list) |   gnomAD 2.1.1 / hg19       |
 +|Structural variants (.vcf.gz, tbi)      |   gnomAD 2.1.1 / hg19       |
  
-** Available modules **+## Applications
  
-    module avail+System provides various graphical and terminal applications for the researchers.
  
 +Additionally to browser, office-suite and text editors the following graphical applications are available:
  
-** Load module **+^Graphical Applications ^Version^ 
 +|MATLAB                             |   R2018b            | 
 +|RStudio                            |   3.5.1             | 
 +|RStudio                            |   3.6.0             | 
 +|RStudio-Server                     |   3.6.0             | 
 +|IGV                                |   2.5.2             |
  
-    module load bowtie2 +^Other Applications ^Version ^Address^ 
- +|[Rstudio-Server](https://www.rstudio.com/products/rstudio/)|   3.6.0|https://solu.uef.fi/rstudio| 
- +|[Singularity Container](https://www.sylabs.io/singularity/)|   3.2.1|             
-** If you wish to Load some specific version number ** +
- +
-    module load python/3.7.3 +
- +
- +
-** Unload module ** +
- +
-    module unload bowtie2 +
- +
- +
-** Save list of loaded modules ** +
- +
-    module save +
- +
- +
-** Restore saved modules ** +
- +
-    module restore +
- +
- +
-### Application location +
-You can quickly go to the application location by writing: +
- +
- +
-    module load bowtie2 +
-    cd $BOWTIE2_ROOT+
  
 +To see the list of terminal application visit the [available applications](https://bioinformatics.uef.fi/guides/available-applications) web page.
  
infrastructure/solu.1560930622.txt.gz · Last modified: 29.10.2019 15:10 (external edit)

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