Bioinformatics Center

User Tools

Site Tools

You are here: home » infrastructure » solu
infrastructure:solu

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revision Previous revision
Next revision 		Previous revision
infrastructure:solu [13.06.2019 20:15]
Juha Kekäläinen 		infrastructure:solu [13.10.2020 12:14] (current)
Juha Kekäläinen
Line 1: Line 1:
 # solu.uef.fi # solu.uef.fi
  
-## Introduction +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).
- +
-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).+
  
 Server address: **solu.uef.fi** Server address: **solu.uef.fi**
Line 14: Line 12:
  
 ## 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
 +
 +URL: [[https://support.illumina.com/sequencing/sequencing_software/igenome.html]]
 +
 +Following reference genomes can be found from the ** /apps/genomes/iGenomes ** folder.
 +
 +^Home sapiens ^Version^
 +|GRCh37                             |   Ensembl       |
 +|GRCh38                             |   NCBI          |
 +|GRCh38Decoy                        |   NCBI          |
 +|hg19                               |   UCSC          |
 +|hg39                               |   UCSC          |
 +
 +^Mus musculus ^Version^
 +|mm9                              |   UCSC       |
 +|mm10                             |   UCSC       |
 +
 +^Rattus norvegicus ^Version^
 +|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
Line 33: Line 70:
 |[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 (12.06.2019) below: 
-    
-   homer/4.9.1                     kallisto/0.43.1 
-   bamtools/2.5.1                  clustalw/2.1            gcc/8.2.0            openmpi/1.10.7-2           r/3.5.1 
-   bamutil/1.0.13                  cufflinks/2.2.1         hisat2/2.1.0         picard/2.18.3              r/3.6.0          (D) 
-   bcftools/1.9                    datamash/1.3            htslib/1.9           plink/1.07                 samtools/1.9 
-   bedtools2/2.27.1                diamond/0.9.21          jdk/11.0.3           prinseq-lite/0.20.4        star/2.6.1b 
-   bowtie/1.2                      fastqc/0.11.7           jdk/12.0.1    (D)    python/2.7.15              tabix/2013-12-16 
-   bowtie2/2.3.4.1-python-3.7.0    fastx-toolkit/0.0.14    matlab/R2018b        python/3.7.0               trimmomatic/0.36 
-   bwa/0.7.17                      gatk/4.0.8.1            mono/5.4.1.7         python/3.7.3        (D)    vcftools/0.1.14 
- 
-## 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 
-'' 
- 
-Unload module: 
-'' 
-module unload bowtie2 
-'' 
- 
-Save list of loaded modules 
-'' 
-module save 
-'' 
- 
-Restore saved modules 
-'' 
-module restore 
-'' 
infrastructure/solu.1560446116.txt.gz · Last modified: 29.10.2019 15:10 (external edit)

Page Tools