Difference between revisions of "Installed Software"
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| [[NAMD]] || 2.9 || [http://www.ks.uiuc.edu/Research/namd/] || Simulation, Chemistry, Biology | | [[NAMD]] || 2.9 || [http://www.ks.uiuc.edu/Research/namd/] || Simulation, Chemistry, Biology | ||
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| − | | [[ | + | | [[Nbody]] || 6 || [http://www.ast.cam.ac.uk/~sverre/web/pages/nbody.htm] || Astronomy |
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<!-- | [[NCO]] || 4.0.9 || [http://nco.sourceforge.net/]|| Data exchange tools || X || | <!-- | [[NCO]] || 4.0.9 || [http://nco.sourceforge.net/]|| Data exchange tools || X || | ||
|- --> | |- --> | ||
| − | | [[ | + | | [[NetCDF]] || in process || [http://www.unidata.ucar.edu/software/netcdf/]|| Data exchange, Tools |
|- | |- | ||
<!-- | [[NetLogo]] || 4.1.3 || [http://ccl.northwestern.edu/netlogo/] || Modeling || X || | <!-- | [[NetLogo]] || 4.1.3 || [http://ccl.northwestern.edu/netlogo/] || Modeling || X || | ||
Revision as of 23:57, 19 September 2012
Note: Cluster Software Upgrade
One of our goals is to provide our users with a consistent, stable, and current software environment. The compute, login, and interactive nodes within the HPC Center have been running CentOS EL 5 (with updates) for over four years. This is a long time in the open source software world. While our software was consistent and stable, it was no longer current. To remedy that shortcoming we upgraded all our systems to RedHat Enterprise Linux 6.3 (RHEL6). The migration was done without interruptions to user jobs as compute nodes were gradually migrated to RHEL6. The migration also afforded us an opportunity to remove software that was no longer used as we only installed software under RHEL6 on request. Therefore, if the software you need is no longer installed please open a support ticket requesting its installation as usual. If you run software you compiled it likely needs to be rebuilt. This is mandatory for all MPI software as we upgraded both MPI implementations and the Intel Compiler Suite on our systems. We also switched to the "Environment Modules" system for making software available. See the modules documentation for more information on how to use the modules system. If you attempt to run a program and it fails it means you have not loaded the appropriate module.
Installed Software List
Last updated 2012-09-19.
Note: Click on the icons to the right of the column headings to sort the table.
| Name | Version [1] | Website | Category |
|---|---|---|---|
| Abyss | 1.3.3, 1.3.4, 1.3.4-mpi | [1] | Biology, NGS |
| ALLPATHS-LG | 42316 | [2] | Biology, NGS |
| Amber | 11, 12 | [3] | Simulation, chemistry |
| Amuse | 6.0 | [4] | Astrophysics |
| Augustus | 2.6 | [5] | Biology, NGS |
| Bamtools | 2.1.1 | [6] | Biology, NGS |
| BamUtil | 1.0.2 | [7] | Biology, NGS |
| BayesRate | 1.3.43 | [8] | Biology, Phylogenetics |
| BEAST | 1.7.2 | [9] | Biology, Phylogenetics |
| BEDTools | 2.16.2 | [10] | Biology, NGS |
| BFAST | 0.7.0 | [11] | Biology, NGS |
| Bismark | 0.7.4 | [12] | Biology, Methylation, NGS |
| Bioconductor | Latest | [13] | Biology, R, Statistics |
| BioPerl | 1.006901 | [14] | Biology, Perl |
| BioPython | 1.59 | [15] | Biology, Python |
| NCBI BLAST | 2.2.26 (+ and legacy) | [16] | Biology, Sequence alignment |
| Blast2go | 2.5.0-20120705 | [17] | Biology, Annotation |
| BLAT | 20120524 | [18] | Biology, Sequence alignment |
| Boost | 1.49.0 | [19] | C++, Library |
| Bwa | 0.6.1 | [20] | Biology, NGS |
| Bowtie | 0.12.8, 2.0.0b6 | [21] | Biology, NGS |
| CAP3 | 20120705 | [22] | Biology, sequence assembly |
| CD-HIT | 4.6 | [23] | Biology, Genomics |
| Charmm | 36a3 | [24] | Simulation, Chemistry |
| CisGenome | 2.0 | [25] | Biology, Genomics, Peak Calling |
| ClustalW | 2.1 | [26] | Biology, Genomics |
| CMake | 2.8.8 | [27] | Programming |
| Consed | 23.0 | [28] | Biology, Genomics |
| CUDA | 4.2 | [29] | Programming, Graphics |
| Cufflinks | 1.3.0, 2.0.0, 2.0.2 | [30] | Biology, NGS |
| Cutadapt | 1.1 | [31] | Biology, NGS |
| DIYABC | many | [32] | Biology, Genomics |
| Dlpoly | 4.03.4 | [33] | Simulation, Biology, Chemistry |
| Dock | 6.5 | [34] | Chemistry, ligand binding prediction |
| emboss | 6.5.7 | [35] | Biology, multi-tool suite |
| Espresso | 5.0.1 | [36] | Modeling, Physics |
| Exonerate | 2.2.0 | [37] | Biology, Genomics |
| FAR | 2.15 | [38] | Biology, Genomics |
| FASTA | 34.26.5 | [39] | Biology, Genomics |
| FastQC | 0.9.6, 0.10.1 | [40] | Biology, NGS |
| Fastx_toolkit | 0.0.13.2 | [41] | Biology, NGS |
| FreeBayes | 0.9.6 | [42] | Biology |
| Garli | 2.0 | [43] | Biology, Phylogenetics |
| GATK | 1.6.9 | [44] | Biology, NGS |
| Gaussian | E01, G03, G09-A.02, G09-C.01 | [45] | Modeling, Computational Chemistry |
| GeneMark | 2012.04 | [46] | Biology, Genomics, Metagenomics |
| Genewise | 2.2.0 | [47] | Biology, Genomics, Annotation |
| Gmap | 20070928, 20120712 | [48] | Biology, Genomics |
| GnuPlot | 4.6.0 | [49] | Graphics, Plotting, Programming |
| Grace | 5.1.22 | [50] | Graphics, plotting, 2D |
| GrADS | 2.0.1 | [51] | Earth Science |
| Gromacs | 4.5.5 | [52] | Chemistry, Modeling, Simulation |
| GSL | 1.15 | [53] | Library, Math, C++, C |
| HaMStR | v8b | [54] | Biology, Genomics |
| HDF5 | 1.8.9 | [55] | Library, Data |
| HMMER3 | 3.0 | [56] | Biology, Genomics |
| HTSeq | 0.5.3p3 | [57] | Biology, NGS |
| HyPhy | 2.1.2.28 | [58] | Biology, Phylogenetics |
| Hypre | 2.8.0b | [59] | Library, Math, Physics |
| Intel Compilers | 11.1, 2012 | [60] | Programming, Compilers |
| Iprscan | 4.8 | [61] | BIology, Genomics |
| Kent | 20120524 | [62] | Biology, NGS |
| Kmer | 1934 | [63] | Biology, NGS |
| Lammps | 25Jul12 | [64] | Simulation |
| Last | 193, 247 | [65] | Biology, Sequence alignment |
| Lastz | 1.02.00 | [66] | Biology, NGS |
| MACS | 1.4.2 | [67] | Biology, ChIP-Seq |
| mafft | 6.903 | [68] | Biology, Multiple sequence alignment |
| Maker | 2.10, 2.25b | [69] | Biology, Annotation, Genomics |
| Maq | 0.7.1 | [70] | Biology, NGS |
| Matlab | 2012a | [71] | Math, Simulation, Programming |
| MATS | 2.1.0 | [72] | BIology, NGS |
| MCNP | 5, 6b2 | [73] | Physics |
| MCNPX | 2.7.0, 2.7.0-i8 | [74] | Physics |
| Meme | 4.8.1 | [75] | Biology, Motifs, Sequence analysis |
| MetaGeneMark | 2012.04 | [76] | Biology, Genomics |
| Midnight Commander | 4.6.1 | [77] | Tools, Utilities |
| Migrate-n | 3.3.0 | [78] | Biology, Population |
| MISO | 0.4.4 | [79] | Biology, NGS |
| MSMBuilder | 2.5.1 | [80] | Molecular Dynamics |
| Molden | 5.0 | [81] | Molecular, electronic structure |
| mosaik | 2.1.33 | [82] | Biology,NGS |
| MrBayes | 3.2.1 | [83] | Biology, Phylogenetics |
| MUMmer | 3.23 | [84] | Biology, Genomics |
| MUSCLE | 3.8.31 | [85] | Biology, Genomics |
| NAMD | 2.9 | [86] | Simulation, Chemistry, Biology |
| Nbody | 6 | [87] | Astronomy |
| NetCDF | in process | [88] | Data exchange, Tools |
| Newbler | 2.6, 2.7 | [89] | Biology, NGS |
| Novoalign | 2.08.02 | [90] | Biology, NGS |
| Parflow | v615 | [91] | Ecology, Modeling |
| PASA | 1.5, r20120625 | [92] | Biology, Genomics |
| PeakSplitter | 1.0 | [93] | Biology, Chip-Seq |
| Perl | 5.16.0 | [94] | Programming, Language |
| PerM | 0.4.0 | [95] | Biology, NGS |
| PhyML | 3.0 | [96] | Biology, Phylogenetics |
| Picard | 1.69, 1.72 | [97] | Biology, NGS |
| Proteinortho | 4.26 | [98] | Biology, Genomics |
| python | 2.6.8, 2.7.3 | [99] | Programming, scripting, language |
| QIIME | 1.5.0 | [100] | Biology, Ecology |
| R | 2.15.0, 2.15.0-mpi, Rmpi/2.15.1 | [101] | Statistics, Programming |
| R8S | 1.71 | [102] | Biology, Evolution |
| RAxML | 7.3.2.0705 | [103] | Biology, Phylogenetics |
| RepeatMasker | 3.3.0 | [104] | Biology, Genomics |
| Reptile | 1.1 | [105] | Biology, NGS, error correction |
| riboPicker | 0.4.3 | [106] | Biology, Sequence |
| samtools | 0.1.16, 0.1.18 | [107] | Biology, NGS |
| SAS | 9.3 | [108] | Statistics, Graphing |
| Schrodinger | 2012 | [109] | Simulation, chemistry |
| SeqPrep | 0.5 | [110] | Biology, NGS |
| SEQuel | 1.0.1 | [111] | Biology, NGS |
| Sickle | 1.200 | [112] | Biology, NGS, quality filter |
| Siesta | 3.0b | [113] | Simulation, Physics, Ab Initio |
| SIFT | 4.0.3b | [114] | Biology, Genomics |
| Silo | 4.7 | [115] | Library, Data |
| Snap | 20100728 | [116] | Biology, Genomics |
| SOAPdenovo | 1.05 | [117] | Biology, NGS |
| SOAPdenovo-Trans | 1.01 | [118] | Biology, NGS |
| SpliceTrap | 0.90.5 | [119] | Biology, NGS, RNA-Seq |
| Sputnik | 1.0 | [120] | Biology, Genomics |
| SRA | 2.1.10 | [121]] | biology, NGS |
| Stacks | 0.9995 | [122] | Biology, Genomics, NGS |
| Structure | 2.3.3 | [123] | Biology, Population |
| tgicl | 2.1 | [124] | Biology, sequencing, clustering |
| Tophat | 1.4.1, 2.0.1 | [125] | Biology, NGS |
| TRF | 4.04 | [126] | Biology, Genomics |
| Trinity | r20120518, r20120608, r20120905 | [127] | Biology, RNA-Seq |
| Twinscan | 4.1.2 | [128] | Biology, Genomics |
| usearch | 5.2.32 | [129] | Biology, Sequence analysis |
| VASP | 4.6.34, 5.2.12 | [130] | Quantum Chemistry, Ab Initio |
| VCFtools | 0.1.9 | [131] | Biology, SNPs |
| velvet | 1.2.06 | [132] | Biology, NGS |
| vmd | 1.9.1 | [133] | Biology, Visualization |
| WebLogo | 3.3 | [134] | Biology, Genomics |
| WDSSII | [135] | Meteorology | |
| wgs | 7.0.1.22 | [136] | Biology, NGS |
| wublast | 2.0 | [137] | Biology, Sequence Alignment |
- ↑ Up to 3 most recent/important releases are listed. See the software wiki pages and the output of "module spider software" for full version listing.
To add a documentation page for a new piece of software installed into /apps please go to Add New App Page.