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infrastructure:solu [30.09.2019 13:54]
Teemu Kuulasmaa 		infrastructure:solu [13.10.2020 10:32]
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]] URL: [[https://support.illumina.com/sequencing/sequencing_software/igenome.html]]
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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
  
 URL: [[https://gnomad.broadinstitute.org/downloads]] URL: [[https://gnomad.broadinstitute.org/downloads]]
  
-Following reference genomes can be found from the ** /apps/genomes/gnomAD ** folder.+Following variants can be found from the ** /research/groups/bioinformaticians/gnomAD-hg19-r2.1.1 ** folder.
  
-^Home sapiens ^Version^ +^Data set ^Version^ 
-|Exome variants (.vcf.bgz)         |   gnomAD 2.1.1 / hg19       | +|Exome variants (.vcf.bgz, tbi)          |   gnomAD 2.1.1 / hg19       | 
-|Genome variants (.vcf.bgz)        |   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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 In the terminal, you can see the list of available software packages by command  In the terminal, you can see the list of available software packages by command 
-'modul avail'. A short list of available applications (19.06.2019) below:+'module avail'. A short list of available applications (13.01.2020) below:
        
-   homer/4.9.1                         kallisto/0.43.1               seqan/2.4.0 +   bamtools/2.5.1                      cufflinks/2.2.1         mothur/1.40.5              r/3.5.3 
-   bamtools/2.5.1                      cufflinks/2.2.1               matlab/R2018b              r/3.6.0          (L,D) +   bamutil/1.0.13                      datamash/1.3            openjdk/11.0.2             r/3.6.0 
-   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           r/3.6.1           (D) 
-   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              samtools/1.9 
-   bedtools2/2.27.1                    fastqc/0.11.7                 picard/2.18.3              star/2.5.4b +   blast-plus/2.7.1                    fastx-toolkit/0.0.14    plink/1.07                 sra-toolkit/2.9.2 
-   bowtie/1.2                          fastx-toolkit/0.0.14          plink/1.07                 star/2.6.1b      (D) +   bowtie/1.2                          gcc/8.2.0               plink/1.90b6.12     (D)    star/2.5.1b 
-   bowtie2/2.3.4.1-python-3.7.0        gcc/8.2.0                     prinseq-lite/0.20.4        tabix/2013-12-16 +   bowtie/1.2.3                 (D)    hisat2/2.1.0            prinseq-lite/0.20.4        star/2.5.4b 
-   breakdancer/master                  hisat2/2.1.0                  python/2.7.15       (L)    trimmomatic/0.36 +   bowtie2/2.3.4.1-python-3.7.0        hmmer/3.0               python/2.7.15              star/2.6.1b       (D) 
-   breakdancer/1.4.5            (D)    htslib/1.9                    python/3.7.0               vcftools/0.1.14 +   breakdancer/master                  htslib/1.9              python/2.7.17              tabix/2013-12-16 
-   bwa/0.7.17                          jdk/11.0.3                    python/3.7.3        (D) +   breakdancer/1.4.5            (D)    jdk/12.0.1              python/3.7.0               trimmomatic/0.36 
-   clustalw/2.1                        jdk/12.0.1           (L,D)    r/3.5.1+   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+## 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) 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:+## Quick tutorial:
  
  
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-### Application location+## Application location 
 You can quickly go to the application location by writing: You can quickly go to the application location by writing:
  
infrastructure/solu.txt · Last modified: 13.10.2020 12:14 by Juha Kekäläinen

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