Sidebar
**This is an old revision of the document!**
Table of Contents
solu.uef.fi
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.
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.
iGenomes
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 |
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 | 3.6.0 | https://solu.uef.fi/rstudio |
| Singularity Container | 3.2.1 |
For the terminal applications use the 'module avail' command. 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