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Software

This page provides a summary of most of the software available on the Hoffman2 cluster

Compilers

Please refer to: Compilers available.

Editors

Emacs | gedit | nano | vi (vim)/evim

Environmental Modules

Please refer to Environmental Modules.

Installations requests

Please refer to: Installation requests.

Applications Packages

For a full list of all packages available please refer to All packages.

Bioinformatics and Biostatistics

Affymetrix Power ToolsANNOVAR | BAMtools | BEDtools | Bowtie |BWACufflinksGalaxy | GATK | IMPUTE | InsPecT | MAQ| Picard ToolsPLINKSAMtoolsSOLARTopHatTreemix | VEGAS

Chemistry and Chemical Engineering

Amber | CASTEP | CP2K | CPMD | Quantum ESPRESSO | GAMESS | GaussianGROMACS | LAMMPS | MOPAC | NAMD | NWChem | OMSSA | OpenBabel | Q-Chem | RasMol | RosettaMatch | XMD | AtomEye | GaussView | Jmol | Molden | VMD

Engineering and Mathematics

ABAQUS | COMSOL | Matlab | NCO netCDF Operators | Octave | OpenSees

Statistics

R | Stata | RStudio

Visualization

AtomEye | GaussView | gnuplot | GRACE | GrADS | Graphviz | IDL | ImageMagick | Jmol | Maple | Mathematica | MATLAB | Molden | NCAR NCL and PyNCL | OpenDX | ParaView | POV-Ray | R | Stata | TECPLOT 360 | VMD | VTK

Languages and Debuggers

ActivePerl | ActiveTcl | ddd | GDC | Java | mono | POP-C++ | Python | Ruby | Tcl/Tk | R | Valgrind

Integrated development environments (IDEs)

RStudio | Eclipse | NetBeans

Programming Libraries

ARPACK | ATLAS | BLAS | Boost C++ | CERNlib | CLHEP | CUDA | FFTW | GNU GSL | HDF | HDF5 | JPEG | LAPACK | Intel MKL | NetCDF | OpenMotif | PETSc | ScaLAPACK | Trilinos | zlib

Misellaneous

CERN ROOT | CMake | cURL | Emacs | Geant | Lynx | MIGRATE-N | SVN subversion | TeXLive | tmux

 

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