Editing BioMicroCenter:Servers (section)

== COMPUTATION ==
=== [http://rous.mit.edu/index.php/Rous.mit.edu_accounts BMC/BCC Computation Cluster (ROUS)] ===
[[ Image:BioMicroCenter_ROUSimage.jpg | thumb | right | 150px | ROUS ]]
Rous is a Linux cluster, initially purchase in September 2009. Rous, named after the Nobel prize winning cancer researcher [http://www.nobelprize.org/nobel_prizes/medicine/laureates/1966/rous-bio.html Peyton Rous] (and not [http://www.urbandictionary.com/define.php?term=R.O.U.S. Rodents Of Unusual Size]) is equipped with a wide range of bioinformatics software. It uses x86 architecture with 160 processing cores and over 500 GB RAM. Rous is the primary server for handling data analysis from Illumina sequencing and for the GALAXY instance at MIT. Users of Rous '''must''' have an account on either BMC-PUB or on Rowley. <BR><BR>

Currently, we are reworking the way the queues on Rous work. In addition to a general queue, similar to what is on Rous now, the new system will have lab specific queue where jobs from that lab will have priority on a specific node (or nodes) of the server. Similar to the data storage model, access to these nodes will be on a charge back basis to recover the cost of the instrumentation. We are currently in the testing phase of this project. <BR><BR>

Some additional useful facts about Rous:
* Rous uses Sun Grid Engine (SGE) to manage jobs. <BR>[http://rous.mit.edu/index.php/SGE_Instructions_and_Tips HOW TO SUBMIT JOBS WITH SGE] <BR>
* Rous uses Modules to handle software packages. <BR> [http://rous.mit.edu/index.php/Managment_of_Software_Packages_with_module HOW TO USE MODULES] <BR>
* Currently, users are limited to 24 simultaneous processes on the server.
* Requests for software changes to Rous should be made to [[BioMicroCenter:People|Stuart Levine]] and [http://rous.mit.edu/index.php/Charlie_Whittaker Charlie Whittaker].


'''We strongly encourage all labs using Illumina sequencing or bioinformatics analysis to have networked data storage. Either Rowley or BMC-PUB storage is *required* to utilize our computer cluster or our GALAXY server.'''

=== Server Software Installed on ROUS ===
A large amount of software is installed on our cluster server. The modules available as of June 2012 include:<BR><BR>
'' Active by default ''
 ----------------------------------------------------------------- /home/software/modulefiles -----------------------------------------------------------------
 allpathslg/46066(default)           cufflinks/1.3.0                     ki-bmc/pipeline_1.1.2               signalp/4.1(default)
 bamtools/1.0.2                      cufflinks/2.0.0                     ki-bmc/pipeline_1.2                 snpeff/2.0.5d
 bedtools/2.15.0(default)            cufflinks/2.0.1                     ki-bmc/pipeline_1.2.1               snpsnift/1.3.4b
 bedtools/2.16.1                     cufflinks/2.0.2                     materialsstudio/6.0                 sra/2.1.10
 bedtools/2.17.0                     cufflinks/2.1.1                     matlab/2011b(default)               tabix/0.2.5(default)
 blast/2.2.27(default)               fasta/35.4.12(default)              muscle/3.8.31(default)              tabix/0.2.6
 bowtie/2.0.0b3(default)             freec/5.7(default)                  novoalign/2.08.03(default)          tmhmm/2.0c(default)
 bowtie2/2.0.0-beta5                 gasv/2012.10.12                     olb/1.9.0                           tophat/1.4.1(default)
 bowtie2/2.0.0-beta6(default)        gatk/1.3-21-gcb284ee                olb/1.9.4(default)                  tophat/2.0.0
 bowtie2/2.0.2                       gatk/1.4-30-gf2ef8d1                pasa/r2012-06-25(default)           tophat/2.0.3
 bowtie2/2.0.3                       gcc/4.8.0(default)                  polysh/0.4(default)                 tophat/2.0.4
 bowtie2/2.0.5                       gmap/2013-01-23                     python/2.7.2(default)               tophat/2.0.6
 bowtie2/2.0.6                       hdf5/1.8.8(default)                 r/2.14.0(default)                   tophat/2.0.7
 bowtie2/2.1.0                       hmmer/3.0(default)                  r/2.14.2                            tophat/2.0.8
 breakdancer/1.1_2011_02_21(default) jre/1.6.0-29(default)               r/2.15.0                            trinityrnaseq/r2012-10-05(default)
 bwa/0.4.6                           ki-bmc/20120516                     r/2.15.3                            trinityrnaseq/r2013-02-25
 bwa/0.6.1(default)                  ki-bmc/pipeline_0.9                 rsem/1.2.3(default)                 ucsc-tools/20120530(default)
 casava/1.8.2                        ki-bmc/pipeline_1.0(default)        samtools/0.1.18(default)            vcftools/0.1.10
 clustalo/1.1.0(default)             ki-bmc/pipeline_1.0.1               samtools/0.1.19                     vcftools/0.1.8a(default)
 cufflinks/1.2.1(default)            ki-bmc/pipeline_1.1                 shera/2012-03-23(default)           wx/2.8.12(default)

'' Active after module add jre ''
 ------------------------------------------------------ /home/software/jre/jre-1.6.0-29/pkg/modulefiles -------------------------------------------------------
 jalview/2.7            picard/1.63            picard/1.72            picard/1.89            varscan/2.3.2(default)

'' Active after module add python ''
 ----------------------------------------------------- /home/software/python/python-2.7.2/pkg/modulefiles -----------------------------------------------------
 HTSeq/0.5.4p1               macs/1.4.2                  numpy/1.6.1(default)        pysam/0.6(default)          virtualenv/1.7(default)
 biopython/1.61              macs/2.0.10_6_6_2012        pip/1.1                     scipy/0.10.0(default)       wxpython/2.8.12.1
 cython/0.15.1(default)      matplotlib/1.1.0(default)   pybedtools/0.6              setuptools/0.6c11(default)
 h5py/2.0.1(default)         mysql-python/1.2.3(default) pybedtools/0.6.2            sicer/1.1


Other packagesare installed but have not yet been converted to module packages. These include:

* BLAT
* GenePattern
* IGV
* MAQ
* MEME
* Velvet