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infrastructure:solu [11.10.2019 19:11] Teemu Kuulasmaa |
infrastructure:solu [13.10.2020 10:32] 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:// | ||
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All the available reference data sets are provided as-is. They are unmodified copies of the original files. | All the available reference data sets are provided as-is. They are unmodified copies of the original files. | ||
- | ### iGenomes | + | ## iGenomes |
URL: [[https:// | URL: [[https:// | ||
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|rn4 | | |rn4 | | ||
- | ### gnomAD | + | ## gnomAD |
URL: [[https:// | URL: [[https:// | ||
- | Following variants can be found from the ** /apps/genomes/gnomAD ** folder. | + | Following variants can be found from the ** /research/groups/ |
^Data set ^Version^ | ^Data set ^Version^ | ||
- | |Exome variants (.vcf.bgz, tbi) | | + | |Exome variants (.vcf.bgz, tbi) | |
- | |Exome calling regions (.interval_list) | | + | |Exome calling regions (.interval list) | |
- | |Genome variants (.vcf.bgz, tbi) | + | |Genome variants (.vcf.bgz, tbi) |
- | |Genome calling regions (.interval_list) | + | |Genome calling regions (.interval list) | |
- | |Structural variants (.vcf.gz, tbi) | | + | |Structural variants (.vcf.gz, tbi) | |
- | ### Applications | + | ## 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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In the terminal, you can see the list of available software packages by command | In the terminal, you can see the list of available software packages by command | ||
- | 'modul avail' | + | 'module |
- | homer/ | + | |
- | bamtools/ | + | |
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- | | + | |
- | | + | blast-plus/2.7.1 |
- | bowtie/1.2 fastx-toolkit/ | + | |
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+ | | ||
+ | | ||
- | ### Lmod Module Environment | + | ## Lmod Module Environment |
Applications are managed with the [Lmod Environment Module System](https:// | Applications are managed with the [Lmod Environment Module System](https:// | ||
- | ### Quick tutorial: | + | ## Quick tutorial: |
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- | ### Application location | + | ## Application location |
You can quickly go to the application location by writing: | You can quickly go to the application location by writing: | ||