HPC Cluster Software Resources: Difference between revisions
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| Trimmomatic || <code>module add trimmomatic</code> || http://www.usadellab.org/cms/index.php?page=trimmomatic<br>http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/TrimmomaticManual_V0.32.pdf || Flexible read trimming tool for Illumina NGS data | | Trimmomatic || <code>module add trimmomatic</code> || http://www.usadellab.org/cms/index.php?page=trimmomatic<br>http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/TrimmomaticManual_V0.32.pdf || Flexible read trimming tool for Illumina NGS data | ||
|- | |- | ||
| Trinity || <code>module add trinity</code> || | | Trinity || <code>module add trinity</code> || https://github.com/trinityrnaseq/trinityrnaseq/wiki/Running-Trinity || Assembles transcript sequences from Illumina RNA-Seq data | ||
|- | |- | ||
| VisIt || <code>module add visit</code> || | | VisIt || <code>module add visit</code> || https://wci.llnl.gov/simulation/computer-codes/visit/manuals || Open Source, interactive, scalable, visualization, animation and analysis tool | ||
|- | |- | ||
| VMD || <code>module add vmd</code> || | | VMD || <code>module add vmd</code> || https://www.ks.uiuc.edu/Research/vmd/current/docs.html || Molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting | ||
|} | |} |
Revision as of 19:27, 21 May 2019
Application Name | Module Command | Application Website/Docs | Notes |
---|---|---|---|
Amber | module add amber |
http://ambermd.org/Manuals.php | Amber is a suite of biomolecular simulation programs |
Athena | module add athena |
https://princetonuniversity.github.io/Athena-Cversion/ | Athena is a grid-based code for astrophysical magnetohydrodynamics (MHD) |
Athena++ | module add athena++ |
https://princetonuniversity.github.io/athena/ | Athena++ is a complete re-write of the Athena astrophysical magnetohydrodynamics (MHD) code in C++ |
Blast+ | module add blast+ |
https://www.ncbi.nlm.nih.gov/books/NBK279690/ | Basic Local Alignment Search Tool |
Cassandra | module add cassandra |
https://cassandra.nd.edu/index.php/documentation | Cassandra is an open source Monte Carlo package |
cuda/8.0 cuda/9.2 cuda/10.0 |
module add cuda module add cuda/8.0 module add cuda/9.2 module add cuda/10.0 |
https://docs.nvidia.com/cuda/ | Default is CUDA 9.2 if using module add cuda
|
cuDNN | module add cudnn |
https://docs.nvidia.com/deeplearning/sdk/cudnn-developer-guide/index.html | - |
ELSA Tutorial | module add elsa-tutorial |
TBA | Used with ELSA SLURM tutorial |
ESPResSo | module add espresso |
http://espressomd.org/wordpress/documentation/ | Extensible Simulation Package for Research on Soft Matter |
FASTX-Toolkit | module add fastx |
http://hannonlab.cshl.edu/fastx_toolkit/commandline.html | FASTQ/A short-reads pre-processing tools |
FFmpeg | module add ffmpeg |
https://ffmpeg.org/ffmpeg.html | ffmpeg is a very fast video and audio converter |
Garli | module add garli |
Website no longer accessible | Genetic Algorithm for Rapid Likelihood Inference |
Gaussian | module add gaussian |
http://gaussian.com/man/ | Electronic structure modeling |
GNUplot | module add gnuplot |
http://www.gnuplot.info/documentation.html | Portable command-line driven graphing utility |
Go | module add go |
https://golang.org/doc/ | Go programming language |
Gromacs | module add gromacs module add gromacs+plumed |
http://manual.gromacs.org/documentation/ https://www.plumed.org/doc-master/user-doc/html/index.html |
Versatile package to perform molecular dynamics |
Hoomd-Blue | module add hoomd-blue |
https://hoomd-blue.readthedocs.io/en/stable/ | General purpose particle simulation toolkit |
JDK | module add jdk |
- | Java. Note: OpenJDK is recommended over this version (Oracle Java) due to licensing issues. OpenJDK is installed in the OS by default so no module is needed. |
Jellyfish | module add jellyfish |
http://www.genome.umd.edu/docs/JellyfishUserGuide.pdf | Fast, parallel k-mer counting for DNA |
Julia | module add julia |
https://docs.julialang.org/en/v1/ | Julia programming language |
LAMMPS | module add lammps |
https://lammps.sandia.gov/doc/Manual.html | Molecular dynamics simulator |
Mathematica | module add mathematica |
Example | Example |
Matlab | module add matlab |
Example | Example |
MOPAC | module add mopac |
http://openmopac.net/manual/ | General-purpose semiempirical molecular orbital package. Primarily used from within the WebMO (http://webmo.hpc.tcnj.edu) system |
MPMC | module add mpmc |
https://github.com/mpmccode/mpmc/wiki | Massively parallel monte carlo |
MrBayes | module add mrbayes |
http://nbisweden.github.io/MrBayes/manual.html | Program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models |
NetPBM | module add netpbm |
http://netpbm.sourceforge.net/doc/ | Toolkit for manipulation of graphic images, including conversion of images between a variety of different formats |
NWChem | CPU - module add nwchem GPU - module add nwchem-cuda |
https://github.com/nwchemgit/nwchem/wiki | Open source high-performance computational chemistry |
Omnia | module add omnia |
https://github.com/omnia-md/omnia-md | High performance, high usability toolkits for predictive biomolecular simulation |
ParaView | module add paraview |
https://www.paraview.org/documentation/ | Open-source, multi-platform data analysis and visualization application. GUI accessed via Open OnDemand (under Interactive Apps) |
pNetCDF | module add pnetcdf |
https://parallel-netcdf.github.io/wiki/Documentation.html | High-performance parallel I/O library for accessing the classic
Unidata's NetCDF files, specifically the CDF 1, 2, and 5 formats |
PRINSEQ | module add prinseq |
http://prinseq.sourceforge.net/manual.html | Filter, reformat, or trim your genomic and metagenomic sequence data |
Python | module add python |
https://www.python.org/doc/ | Programming language that lets you work more quickly and integrate your systems more effectively |
R | module add R |
https://cran.r-project.org/manuals.html | Free software environment for statistical computing and graphics |
RStudio Server | module add rstudio_singularity |
https://resources.rstudio.com/ | Integrated development environment (IDE) for R. Web front-end accessed via Open OnDemand (under Interactive Apps) |
SageMath | module add sagemath |
http://doc.sagemath.org/ | Free open-source mathematics software system. Web version accessed via Jupyter Notebook in Open OnDemand (under Interactive Apps) |
SAS | module add sas |
SAS docs | Open analytics platform accessible from the interface or coding language of your choice |
SOAPDenovo2 | module add soapdenovo2 |
https://github.com/aquaskyline/SOAPdenovo2#how-to-use-it | Novel short-read assembly method that can build a de novo draft assembly for the human-sized genomes. The program is specially designed to assemble Illumina GA short reads. It creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost effective way |
Sondovac | module add sondovac |
https://github.com/V-Z/sondovac/wiki/Documentation | Script to create orthologous low-copy nuclear probes from
transcriptome and genome skim data for target enrichment |
SOP-GPU | module add sop-gpu |
Example | Self Orginized Polymer Model fully implemented on a GPU. A scientific software package designed to perform Langevin Dynamics Simulations of the mechanical or thermal unfolding, and mechanical pulling/indentation of large biomolecular systems in the experimental subsecond (millisecond-to-second) timescale |
SPAdes | module add spades |
https://github.com/ablab/spades | St. Petersburg genome assembler – is an assembly toolkit containing various assembly pipelines |
Swift | module add swift |
http://swift-lang.org/docs/index.php | Simple tool for fast, easy scripting on big machines |
Transcriptomics | module add transcriptomics |
Example | Example |
Trimmomatic | module add trimmomatic |
http://www.usadellab.org/cms/index.php?page=trimmomatic http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/TrimmomaticManual_V0.32.pdf |
Flexible read trimming tool for Illumina NGS data |
Trinity | module add trinity |
https://github.com/trinityrnaseq/trinityrnaseq/wiki/Running-Trinity | Assembles transcript sequences from Illumina RNA-Seq data |
VisIt | module add visit |
https://wci.llnl.gov/simulation/computer-codes/visit/manuals | Open Source, interactive, scalable, visualization, animation and analysis tool |
VMD | module add vmd |
https://www.ks.uiuc.edu/Research/vmd/current/docs.html | Molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting |