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infrastructure:solu [14.03.2020 13:58]
Teemu Kuulasmaa [Available reference data set] 		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]].
  
  
-### Available reference data set+## Available reference data set
  
 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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 |[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 (13.01.2020) below: +
-    +
-   bamtools/2.5.1                      cufflinks/2.2.1         mothur/1.40.5              r/3.5.3 +
-   bamutil/1.0.13                      datamash/1.3            openjdk/11.0.2             r/3.6.0 +
-   bcftools/1.9                        diamond/0.9.21          openmpi/1.10.7-2           r/3.6.1           (D) +
-   bedtools2/2.27.1                    fastqc/0.11.7           picard/2.18.3              samtools/1.9 +
-   blast-plus/2.7.1                    fastx-toolkit/0.0.14    plink/1.07                 sra-toolkit/2.9.2 +
-   bowtie/1.2                          gcc/8.2.0               plink/1.90b6.12     (D)    star/2.5.1b +
-   bowtie/1.2.3                 (D)    hisat2/2.1.0            prinseq-lite/0.20.4        star/2.5.4b +
-   bowtie2/2.3.4.1-python-3.7.0        hmmer/3.0               python/2.7.15              star/2.6.1b       (D) +
-   breakdancer/master                  htslib/1.9              python/2.7.17              tabix/2013-12-16 +
-   breakdancer/1.4.5            (D)    jdk/12.0.1              python/3.7.0               trimmomatic/0.36 +
-   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 +
- +
-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.1584187114.txt.gz · Last modified: 14.03.2020 13:58 by Teemu Kuulasmaa

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