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infrastructure:solu [26.09.2019 13:33] Teemu Kuulasmaa |
infrastructure:solu [13.10.2020 12:14] Juha Kekäläinen |
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Server address: **solu.uef.fi** | Server address: **solu.uef.fi** | ||
- | ### System specs | + | ## System specs |
- CPU: 48 Cores (4 x AMD Opteron(tm) Processor 6348) | - CPU: 48 Cores (4 x AMD Opteron(tm) Processor 6348) | ||
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- OS: CentOS 7 Linux | - OS: CentOS 7 Linux | ||
- | ### Storage | + | ## Storage |
Server is connected to the storage space provided by the [UEF IT Services for Research](https:// | Server is connected to the storage space provided by the [UEF IT Services for Research](https:// | ||
- | ### iGenomes | + | |
+ | ## 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:// | ||
Following reference genomes can be found from the ** / | Following reference genomes can be found from the ** / | ||
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^Mus musculus ^Version^ | ^Mus musculus ^Version^ | ||
- | |mm9 | + | |mm9 | |
- | |mm10 | + | |mm10 |
^Rattus norvegicus ^Version^ | ^Rattus norvegicus ^Version^ | ||
- | |rn4 | + | |rn4 | |
- | ### Applications | + | ## gnomAD |
+ | |||
+ | 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. | System provides various graphical and terminal applications for the researchers. | ||
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|[Singularity Container](https:// | |[Singularity Container](https:// | ||
- | In the terminal, you can see the list of available software packages by command | + | To see the list of terminal application visit the [available applications](https:// |
- | 'modul avail' | + | |
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- | ### 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:// | + | |
- | + | ||
- | ### Quick tutorial: | + | |
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- | + | ||
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- | ** Available modules ** | + | |
- | + | ||
- | module avail | + | |
- | + | ||
- | + | ||
- | ** Load module ** | + | |
- | + | ||
- | module load bowtie2 | + | |
- | + | ||
- | + | ||
- | ** If you wish to Load some specific version number ** | + | |
- | + | ||
- | module load python/ | + | |
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- | + | ||
- | ** Unload module ** | + | |
- | + | ||
- | module unload bowtie2 | + | |
- | + | ||
- | + | ||
- | ** Save list of loaded modules ** | + | |
- | + | ||
- | module save | + | |
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- | ** Restore saved modules ** | + | |
- | + | ||
- | module restore | + | |
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- | + | ||
- | ### Application location | + | |
- | You can quickly go to the application location by writing: | + | |
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- | + | ||
- | module load bowtie2 | + | |
- | cd $BOWTIE2_ROOT | + | |