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Table of Contents
BIX servers
Hostnames
- bix1.uef.fi
- bix2.uef.fi
- bix3.uef.fi
System Specs
Three identical Dell Blade servers with the following specs:
- Dell Blade M620 Server
- 2 x Intel(R) Xeon(R) CPU E5-2650 0 2.00 GHz
- 192 GB DDR3 EEC 1333 MHz
- CentOS 7.2
- Connected to bio-fs1.uef.fi fileserver
Remote Connections
User can take remote connection to the BIX-servers from the university network with SSH applications or with Remote Desktop Connection application. Good choices for the SSH are WinSCP for file transfer and PuTTy for the terminal access.
Remote Desktop Connection comes with the Windows operating system and it can be found from the Windows start menu.
From the home or from the eduroam network user must use codon.uef.fi SSH Gateway server to connect BIX-servers.
It is also possible to connect BIX-servers with the Citrix Receiver.
Applications
Applications are installed into /usr/local/stow folder and symbolic links are made to /usr/local/bin folder with Stow utility. Java-applications are installed into /usr/local/java folder. Also Homer (/usr/local/homer) and MATLAB (/usr/local/MATLAB) have custom locations.
Different versions of applications (if available) can be loaded to current environment with *module* command. For example module load python/3.5.1.
To see all available modules use module avail command.
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Application / Tool / Library | Latest Version | Absolute Path ——————————–|——————|————————————————-
| AGE | 0.4 | /usr/local/stow/AGE/noomp/| |Bamtools | 2.4.0 | /usr/local/stow/bamtools/2.4.0/| |BCF Tools | 1.3.1 | /usr/local/stow/bcftools/1.3.1/| |BisSNP | 0.82.2 | /usr/local/java/BisSNP/0.82.2/| |Bowtie 1 | 1.1.2 | /usr/local/stow/bowtie/1.1.2/| |Bowtie 2 | 2.2.9 | /usr/local/stow/bowtie/2.29/| |BWA | 0.7.13 | /usr/local/stow/bwa/0.7.13/| |CGATools | 1.8.0.1 | /usr/local/stow/cgatools/1.8.0.1/| |Clustal-Omega | 1.21 | /usr/local/stow/clustal-omega/1.2.1/| |Cufflinks | 2.2.1 | /usr/local/stow/cufflinks/2.2.1/| |Cytoscape | 3.4.0 | /usr/local/java/cytoscape/3.4.0/| |Denovogear | 1.1.1 | /usr/local/stow/denovogear/1.1.1/| |FastQC | 0.11.5 | /usr/local/stow/fastqc/0.11.5/| |Fastx Toolkit | 0.0.14 | /usr/local/stow/fastxtoolkit/0.0.14/ |
| FindTranslocations | Git 16.04.2016 | /usr/local/stow/FindTranslocations/git/ |
| Freebayes | 1.0.2-16 | /usr/local/stow/freebayes/v1.0.2-16-gd466dde/ |
| FSL | 5.0.9 | /usr/local/stow/fsl/5.0.9/ |
| Genome Analysis Toolkit (GATK) | 3.5 | /usr/local/java/GATK/3.5/ |
| HiCUP | 0.5.8 | /usr/local/stow/hicup/0.5.8/ |
| HISAT | 2.0.3-beta | /usr/local/stow/hisat/2.0.3-beta/ |
| HMMER | 3.1b2 | /usr/local/stow/hmmer/3.1b2/ |
| Homer | 4.8 | /usr/local/homer/4.8/ |
| IGV | 2.3.72 | /usr/local/java/IGV/2.3.72/ |
| Kallisto | 0.42.5 | /usr/local/stow/kallisto/0.42.5/ |
| Lumpy | 0.2.13 | /usr/local/stow/lumpy/0.2.13/ |
| MACS | 1.4.2 | Python 2.7 |
| MACS2 | 2.1.1 | Python 2.7 |
| Manta | 0.29.6 | /usr/local/stow/manta/0.29.6/ |
| MATLAB | R2015b | /usr/local/MATLAB/R2015b/ |
| MetaSV | 0.5.2 | /usr/lib/python2.7/site-packages/metasv/ |
| mlpack | 2.0.1 | /usr/local/stow/mlpack/2.0.1/ |
| Mothur | 1.37 | /usr/local/stow/mothur/1.37/ |
| Mrtrix3 | Git 04.05.2016 | /usr/local/stow/mrtrix3/git/ |
| NGSQC Toolkit | 2.3.3 | /usr/local/stow/NGSQCToolkit/2.3.3/ |
| Picard-Tools | 2.2.2 | /usr/local/java/picard/2.2.2/ |
| PLINK | 0.190b3p | /usr/local/stow/plink/1.90b3p/ |
| Pypette | 0.7.1 | /usr/local/stow/pypette-0.7.1/ |
| Python | 3.5.1 | /usr/local/stow/python/3.5.1/ |
| R 3.2.3 | 3.2.3 | default |
| R 3.3.1 | 3.3.1 | /usr/local/stow/R/3.3.1/ |
| SAINTexpress | 3.62014-12-04 | /usr/local/stow/SAINTexpress/3.62014-12-04/ | |
| Sambamba | 0.6.0 | /usr/local/stow/sambamba/0.6.0/ |
| SPAdes | 3.7.1 | /usr/local/stow/SPAdes/3.7.1/ |
| SRA Toolkit | 2.6.2 | /usr/local/stow/sratoolkit/2.6.2/ |
| STAR | 2.5.1b | /usr/local/stow/STAR/2.5.1b/ |
| Stringtie | 1.2.2 | /usr/local/stow/stringtie/1.2.2/ |
| TopHat | 1.4.1 | /usr/local/stow/tophat/1.4.1/ |
| TopHat | 2.1.1 | /usr/local/stow/tophat/2.1.1/ |
| Trimmomatic | 0.33 | /usr/local/java/Trimmomatic/0.33/ |
| UCSC Tools | /usr/local/stow/ucsc_tools/ | |
| VCFTools | 0.1.13 | /usr/local/stow/vcftools/0.1.13/ |
| WebLogo | 2.8.2 | /usr/local/stow/weblogo/2.8.2/ |
| Weka | 3.6.12 | /usr/local/java/weka/3.6.12/ |