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infrastructure:solu [10.06.2019 15:01]
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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 - CPU: 48 Cores (4 x AMD Opteron(tm) Processor 6348) - CPU: 48 Cores (4 x AMD Opteron(tm) Processor 6348)
 - RAM: 768 GB DDR3 - RAM: 768 GB DDR3
-- OS: CentOS 7+- OS: CentOS 7 Linux
  
 ## 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 Application ^Version^ +## iGenomes
-|MATLAB                             |   R2018b            | +
-|RStudio                            |   3.5.1             | +
-|RStudio                            |   3.6.0             | +
-|RStudio-Server                     |   3.6.0             | +
-|IGV                                |   2.5.2             |+
  
-Rstudio-Server is available at [https://solu.uef.fi/rstudio](https://solu.uef.fi/rstudio)+URL: [[https://support.illumina.com/sequencing/sequencing_software/igenome.html]]
  
-For the terminal applications use the 'module avail' command. Short list of available applications (06.06.2019) below: +Following reference genomes can be found from the ** /apps/genomes/iGenomes ** folder.
-    +
-   homer/4.9.1                     kallisto/0.43.1 +
-   bamtools/2.5.1                  clustalw/2.1            hisat2/2.1.0            picard/2.18.3                   python/3.7.0     (D) +
-   bamutil/1.0.13                  cufflinks/2.2.1         htslib/1.9              plink/1.07                      r/3.5.1 +
-   bcftools/1.9                    datamash/1.3            jdk/11.0.3              prinseq-lite/0.20.4             r/3.6.0          (D) +
-   bedtools2/2.27.1                diamond/0.9.21          jdk/12.0.1       (D)    py-numpy/1.15.2-python-3.7.0    samtools/1.9 +
-   bowtie/1.2                      fastqc/0.11.7           matlab/R2018b           py-pip/10.0.1-python-3.7.0      star/2.6.1b +
-   bowtie2/2.3.4.1-python-3.7.0    fastx-toolkit/0.0.14    mono/5.4.1.7            py-scipy/1.1.0-python-3.7.0     tabix/2013-12-16 +
-   bwa/0.7.17                      gcc/8.2.0               openmpi/1.10.7-2        python/2.7.15                   trimmomatic/0.36 +
-   +
  
-## Lmod Module Environment+^Home sapiens ^Version^ 
 +|GRCh37                             |   Ensembl       | 
 +|GRCh38                             |   NCBI          | 
 +|GRCh38Decoy                        |   NCBI          | 
 +|hg19                               |   UCSC          | 
 +|hg39                               |   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)+^Mus musculus ^Version^ 
 +|mm9                              |   UCSC       | 
 +|mm10                             |   UCSC       |
  
-Quick tutorial:+^Rattus norvegicus ^Version^ 
 +|rn4                              |   UCSC       |
  
 +## gnomAD
  
-Available modules: +URL: [[https://gnomad.broadinstitute.org/downloads]]
-'' +
-module avail +
-''+
  
-Load module: +Following variants can be found from the ** /research/groups/bioinformaticians/gnomAD-hg19-r2.1.1 ** folder. 
-'' + 
-module load bowtie2 +^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       | 
 + 
 +## Applications 
 + 
 +System provides various graphical and terminal applications for the researchers. 
 + 
 +Additionally to browser, office-suite and text editors the following graphical applications are available: 
 + 
 +^Graphical Applications ^Version^ 
 +|MATLAB                             |   R2018b            | 
 +|RStudio                            |   3.5.1             | 
 +|RStudio                            |   3.6.0             | 
 +|RStudio-Server                     |   3.6.0             | 
 +|IGV                                |   2.5.2             |
  
-Unload module: +^Other Applications ^Version ^Address^ 
-'' +|[Rstudio-Server](https://www.rstudio.com/products/rstudio/)|   3.6.0|https://solu.uef.fi/rstudio| 
-module unload bowtie2 +|[Singularity Container](https://www.sylabs.io/singularity/)|   3.2.1|             
-''+
  
-Save list of loaded modules +To see the list of terminal application visit the [available applications](https://bioinformatics.uef.fi/guides/available-applications) web page.
-'' +
-module save +
-''+
  
-Restore saved modules 
-'' 
-module restore 
-'' 
infrastructure/solu.1560168069.txt.gz · Last modified: 29.10.2019 15:10 (external edit)

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