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Sirius User Guide

* Still under construction, but here’s a little info about Sirius:

Sirius is a single CentOS 6.5 Linux large memory server shared among bioinformatics researchers. This system is currently configured with
64 Intel Xeon E5-4640 cores + 757 GB RAM

A somewhat outdated wiki page for Sirius is available here: http://sirius.hpc.rutgers.edu

Connecting to Sirius

If you are on any of the legacy Rutgers campuses, then:

ssh [your NetID]@sirius.hpc.rutgers.edu

If you are off-campus or on the UMDNJ campus, you will have to use the vpn to reach Sirius:

Details about Rutgers vpn can be found: https://oit.rutgers.edu/vpn

VPN software to download can be found here: https://software.rutgers.edu/product/3085

and instructions can be found here: https://wiki.td.rutgers.edu/wiki/Category:VPN

Once the VPN is installed and turned on, ssh as above:

ssh [your NetID]@sirius.hpc.rutgers.edu

Software currently installed on Sirius

Sirius uses the modules system to manage software packages. To see what’s installed, use the module avail command:

$ module avail

-------------------------------------------- /usr/share/Modules/modulefiles --------------------------------------------
dot         module-git  module-info modules     null        use.own

--------------------------------------------------- /etc/modulefiles ---------------------------------------------------
abyss/1.5.2               compat-openmpi-psm-x86_64 java/1.7.0_91             python/2.6.6
AmberTools/15             compat-openmpi-x86_64     java/1.8.0_60             python/2.7.10
autodock/          coot/0.7.2                java/1.8.0_65             python/2.7.8
autodock/4.2.6            coot/0.8.1                java/1.8.0_73             qiime/1.8.0
autodock_vina/1.1.2       cufflinks/2.1.1           knime/2.11.3              rna-star/2.3.0
bcl2fastq/1.8.4           cufflinks/2.2.1           knime/3.1.1               rna-star/2.4.2a
bcl2fastq2/      eclipse/4.4.2             leadit/2.1.8              rna-star/2.5.2a
bedtools2/2.19.1          emboss/6.6.0              llvm/3.3                  RSEM/1.2.19
bedtools2/2.20.1          FastQC/0.11.2             llvm/3.4.2                RStudio/0.98.1102
bedtools2/2.22.0          FASTX-Toolkit/0.0.14      MACS/1.4.3                samtools/0.1.19
bedtools2/2.22.1          gcc/4.7.4                 MACS2/      samtools/1.1
bedtools2/2.24.0          gcc/4.8.4                 matlab/R2015a             samtools/1.2
binutils/2.27             gcc/4.8.5                 MEME/4.10.0               SAS/9.4
blasr/1.3.1               gcc/4.9.2                 mgltools/1.5.6(default)   SNP2HLA/1.0.3
bowtie2/2.1.0             gcc/4.9.3                 mgltools/1.5.7rc1         sybyl-x/2.1.1
bowtie2/2.2.0             gdb/7.8.1                 MISO/0.5.3                tophat/2.0.10
bowtie2/2.2.1             glibc/2.17                moe/2014.0901             tophat/2.0.11
bowtie2/2.2.3             goldsuite/5.2             moe/2015                  tophat/2.0.12
bowtie2/2.2.4             GROMACS/4.6.5             ncbi-blast/2.2.30+        tophat/2.0.13
bowtie2/2.2.5             HMMER/3.1b2               ngsplot/2.47.1            tophat/2.1.0
CHANCE                    IGV/2.3.32                openbabel/2.3.2           transabyss/1.5.2
chimera/1.10              IGV/2.3.40                openmpi-1.4-psm-x86_64    Trimmomatic/0.36
chimera/1.10.1            intel/14.0.3              openmpi-1.4-x86_64        trinityrnaseq/2.0.6
chimera/1.10.2(default)   intel/14.0.4              openmpi-1.5.3-psm-x86_64  Trinotate/2.0.2
chimera/1.8               intel/15.0.1              openmpi-1.5.3-x86_64      vmd/1.9.1
chimera/1.8.1             intel/15.0.2              pandaseq/20140929         WaveCNV
chimera/1.9               intel/15.0.3              phenix/1.9                weka/3.6.10
clc-workbench/8.5         java/1.6.0_45             PhyloCSF/20151123         weka/3.6.11
clc-workbench/9.0.1       java/1.7.0_79             PLINK/1.07

To load a software module (to setup your command shell environment for using that software) you can use the module load command:

$ module load trinityrnaseq/2.0.6

Now, I can see that the Trinity Perl script is included in my $PATH, so I can run it by simply using the Trinity command:

$ which Trinity