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

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

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

All the available reference data sets are provided as-is. They are unmodified copies of the original files.

URL: https://support.illumina.com/sequencing/sequencing_software/igenome.html

Following reference genomes can be found from the /apps/genomes/iGenomes folder.

URL: https://gnomad.broadinstitute.org/downloads

Following variants can be found from the /research/groups/bioinformaticians/gnomAD-hg19-r2.1.1 folder.

System provides various graphical and terminal applications for the researchers.

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

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

Applications are managed with the Lmod Environment Module System. Guide for the Lmod can be found here

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

You can quickly go to the application location by writing:

module load bowtie2
cd $BOWTIE2_ROOT