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infrastructure:solu [21.09.2019 15:30]
Teemu Kuulasmaa 		infrastructure:solu [13.10.2020 12:14] (current)
Juha Kekäläinen
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 # solu.uef.fi # solu.uef.fi
  
-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).+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).
  
 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]].
 +
 +
 +## Available reference data set
 +
 +All the available reference data sets are provided as-is. They are unmodified copies of the original files. 
  
 ## iGenomes ## iGenomes
 +
 +URL: [[https://support.illumina.com/sequencing/sequencing_software/igenome.html]]
  
 Following reference genomes can be found from the ** /apps/genomes/iGenomes ** folder. Following reference genomes can be found from the ** /apps/genomes/iGenomes ** folder.
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 ^Mus musculus ^Version^ ^Mus musculus ^Version^
-|mm9                             |   UCSC       | +|mm9                              |   UCSC       | 
-|mm10                             |   UCSC          |+|mm10                             |   UCSC       |
  
 ^Rattus norvegicus ^Version^ ^Rattus norvegicus ^Version^
-|rn4                             |   UCSC       |+|rn4                              |   UCSC       | 
 + 
 +## gnomAD 
 + 
 +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       |
  
 ## Applications ## Applications
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 |[Singularity Container](https://www.sylabs.io/singularity/)|   3.2.1|              |[Singularity Container](https://www.sylabs.io/singularity/)|   3.2.1|             
  
- +To see the list of terminal application visit the [available applications](https://bioinformatics.uef.fi/guides/available-applications) web page.
- +
-For the terminal applications use the 'module avail' command. Short list of available applications (19.06.2019) below: +
-    +
-   homer/4.9.1                         kallisto/0.43.1               seqan/2.4.0 +
-   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 +
- +
-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) +
- +
-## Quick tutorial: +
- +
- +
- +
-** Available modules ** +
- +
-    module avail +
- +
- +
-** Load module ** +
- +
-    module load bowtie2 +
- +
- +
-** 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 +
  
infrastructure/solu.1569069056.txt.gz · Last modified: 29.10.2019 15:10 (external edit)

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