This shows you the differences between two versions of the page.
Both sides previous revision Previous revision Next revision | Previous revision | ||
infrastructure:solu [06.06.2019 10:46] 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:// |
- | Solu (finnish word for Cell) Computing | + | Server |
- | + | ||
- | Address of the server: | + | |
- | *solu.uef.fi* | + | |
## System specs | ## System specs | ||
- | - CPU: 4 x AMD Opteron(tm) Processor 6348 | + | - CPU: 48 Cores (4 x AMD Opteron(tm) Processor 6348) |
- RAM: 768 GB DDR3 | - RAM: 768 GB DDR3 | ||
- | - OS: CentOS 7 | + | - OS: CentOS 7 Linux |
- | ## Applications | + | ## Storage |
- | System provides various graphical and terminal applications | + | Server is connected to the storage space provided by the [UEF IT Services |
- | Additionally to browser, office-suite and text editors the following graphical applications are available: | ||
- | ^Graphical Application ^Version^ | + | ## Available reference data set |
- | |MATLAB | + | |
- | |RStudio | + | |
- | |RStudio | + | |
- | |IGV | | + | |
- | For the updated terminal applications use the ' | + | All the available reference data sets are provided as-is. They are unmodified copies |
- | | + | ## iGenomes |
- | | + | |
- | | + | |
- | | + | |
- | | + | |
- | | + | |
- | | + | |
- | | + | |
- | | + | |
- | + | ||
- | ## Lmod Module Environment | + | URL: [[https:// |
- | Applications are managed with the [Lmod Environment Module System](https:// | + | Following reference genomes |
- | Quick tutorial: | + | ^Home sapiens ^Version^ |
+ | |GRCh37 | ||
+ | |GRCh38 | ||
+ | |GRCh38Decoy | ||
+ | |hg19 | ||
+ | |hg39 | ||
+ | ^Mus musculus ^Version^ | ||
+ | |mm9 | | ||
+ | |mm10 | ||
- | Available modules: | + | ^Rattus norvegicus ^Version^ |
- | '' | + | |rn4 | |
- | module avail | + | |
- | '' | + | |
- | Load module: | + | ## gnomAD |
- | '' | + | |
- | module load bowtie2 | + | URL: [[https:// |
- | '' | + | |
+ | Following variants can be found from the ** / | ||
+ | |||
+ | ^Data set ^Version^ | ||
+ | |Exome variants (.vcf.bgz, tbi) | | ||
+ | |Exome calling regions (.interval list) | | ||
+ | |Genome variants (.vcf.bgz, tbi) | ||
+ | |Genome calling regions (.interval list) | | ||
+ | |Structural variants (.vcf.gz, tbi) | | ||
+ | |||
+ | ## 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 | ||
+ | |RStudio | ||
+ | |RStudio | ||
+ | |RStudio-Server | ||
+ | |IGV | | ||
- | Unload module: | + | ^Other Applications ^Version ^Address^ |
- | '' | + | |[Rstudio-Server](https:// |
- | module unload bowtie2 | + | |[Singularity Container](https:// |
- | '' | + | |
- | Save list of loaded modules | + | To see the list of terminal application visit the [available applications](https:// |
- | '' | + | |
- | module save | + | |
- | '' | + | |
- | Restore saved modules | ||
- | '' | ||
- | module restore | ||
- | '' |