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infrastructure:solu [30.09.2019 13:32]
Teemu Kuulasmaa 		infrastructure:solu [13.10.2020 12:14] (current)
Juha Kekäläinen
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 Server address: **solu.uef.fi** Server address: **solu.uef.fi**
  
-### System specs+## System specs
  
 - CPU: 48 Cores (4 x AMD Opteron(tm) Processor 6348) - CPU: 48 Cores (4 x AMD Opteron(tm) Processor 6348)
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 - OS: CentOS 7 Linux - 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]].
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 ## Available reference data set ## Available reference data set
  
-### iGenomes+All the available reference data sets are provided as-is. They are unmodified copies of the original files.  
 + 
 +## 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+## gnomAD
  
-Following reference genomes can be found from the ** /apps/genomes/gnomAD ** folder.+URL: [[https://gnomad.broadinstitute.org/downloads]]
  
-^Home sapiens ^Version^ +Following variants can be found from the ** /research/groups/bioinformaticians/gnomAD-hg19-r2.1.1 ** folder. 
-|All chromosomes VCF (.tbi)         |   hg19       |+ 
 +^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
  
 System provides various graphical and terminal applications for the researchers. System provides various graphical and terminal applications for the researchers.
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 |[Singularity Container](https://www.sylabs.io/singularity/)|   3.2.1|              |[Singularity Container](https://www.sylabs.io/singularity/)|   3.2.1|             
  
-In the terminal, you can see the list of available software packages by command  +To see the list of terminal application visit the [available applications](https://bioinformatics.uef.fi/guides/available-applications) web page.
-'modul avail'. A 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.1569839524.txt.gz · Last modified: 29.10.2019 15:10 (external edit)

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