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infrastructure:solu [11.10.2019 19:13]
Teemu Kuulasmaa
infrastructure:solu [14.03.2020 14:05] (current)
Teemu Kuulasmaa
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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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 All the available reference data sets are provided as-is. They are unmodified copies of the original files. ​ 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]] URL: [[https://​support.illumina.com/​sequencing/​sequencing_software/​igenome.html]]
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 |rn4                              |   ​UCSC ​      | |rn4                              |   ​UCSC ​      |
  
-### gnomAD+## gnomAD
  
 URL: [[https://​gnomad.broadinstitute.org/​downloads]] URL: [[https://​gnomad.broadinstitute.org/​downloads]]
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 |Structural variants (.vcf.gz, tbi)      |   ​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:+'modul 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.                         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.             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.1570810407.txt.gz · Last modified: 29.10.2019 15:10 (external edit)