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infrastructure:solu

solu.uef.fi

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.

Server address: solu.uef.fi

System specs

  • CPU: 48 Cores (4 x AMD Opteron™ Processor 6348)
  • RAM: 768 GB DDR3
  • OS: CentOS 7 Linux

Storage

Server is connected to the storage space provided by the UEF IT Services for Research. More information can be found from the 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

System provides various graphical and terminal applications for the researchers.

Additionally to browser, office-suite and text editors the following graphical applications are available:

Graphical Applications Version
MATLAB R2018b
RStudio 3.5.1
RStudio 3.6.0
RStudio-Server 3.6.0
IGV 2.5.2
Other Applications Version Address
Rstudio-Server 3.6.0https://solu.uef.fi/rstudio
Singularity Container 3.2.1

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:

 
 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. Guide for the Lmod can be found here

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.txt · Last modified: 29.10.2019 15:10 (external edit)