HPC Cluster Software Resources: Difference between revisions

Latest revision as of 13:35, 29 May 2024

The ELSA HPC cluster utilizes the Lmod environment module system. Lmod allows you to load and unload various environments to support multiple applications. It also allows you to select among different versions of an application depending on your requirements, e.g. load a Python 2.7.12 environment for application "A" and then load a Python 3.6.0 environment for application "B."

When working interactively at the Linux command-line (e.g. on a login node or dev node), you can run the module add module_name at the shell prompt to load a particular environment. You should also include the appropriate module add module_name command(s) in your SLURM submission script. Use the module avail command at the Linux shell prompt to list all available modules. If you do not specify the version number when adding a module, it will usually load the newest version unless otherwise noted, e.g. module add python is equivalent to module add python/3.6.0.

For more information on working with Lmod modules on the ELSA cluster see the dedicated ELSA Lmod tutorial page.

Note: This software listing may be incomplete or contain software that is no longer available. It will be updated in the future. Use the module avail command to get the most updated list of available software packages.

Application Name	Module Command	Application Website/Docs	Notes
ABySS	`module add abyss`	https://docs.anaconda.com/anaconda/	ABySS is a de novo sequence assembler intended for short paired-end reads and large genomes
Alphafold2	`module`	TBD	TBD
Amber	`module add amber`	http://ambermd.org/Manuals.php	Amber is a suite of biomolecular simulation programs
anaconda	`module add anaconda3`	https://docs.anaconda.com/anaconda/	Anaconda is a package manager, an environment manager, a Python/R data science distribution, and a collection of over 7,500+ open-source packages
ASTRAL	`module add astral`	https://github.com/smirarab/ASTRAL/blob/master/astral-tutorial.md	ASTRAL is a java program for estimating a species tree given a set of unrooted gene trees
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++
Autodock Vina	`module`	TBD	TBD
Blast+	`module add blast+`	https://www.ncbi.nlm.nih.gov/books/NBK279690/	Basic Local Alignment Search Tool
Blender	`module`	TBD	TBD
Cassandra	`module add cassandra`	https://cassandra.nd.edu/index.php/documentation	Cassandra is an open source Monte Carlo package
ChimeraX	`module`	TBD	TBD
CIAO	`module`	TBD	TBD
CUDA	`module add cuda` `module add cuda/8.0` `module add cuda/10.1` `module add cuda/10.2` `module add cuda/11.4` `module add cuda/11.7` `module add cuda/11.8`	https://docs.nvidia.com/cuda/	Default is CUDA 11.4 if using `module add cuda` CUDA 11.8 contains TensorRT 8.6.1.6 and cuDNN 8.9.5.29
ddcMD	`module add ddcmd`	https://github.com/LLNL/ddcMD	A fully GPU-accelerated molecular dynamics program for the Martini force field
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
FastQC	`module add fastqc`	TBD	TBD
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`	https://molevol.mbl.edu/index.php/Garli_FAQ	Genetic Algorithm for Rapid Likelihood Inference
Gaussian	`module add gaussian`	http://gaussian.com/man/	Electronic structure modeling
GaussView	-	http://gaussian.com/wp-content/uploads/dl/gv6.pdf	Graphical interface used with Gaussian which aids in the creation of Gaussian input files, enables the user to run Gaussian calculations from a graphical interface without the need for using a command line instruction, and helps in the interpretation of Gaussian output. GUI accessed via Open OnDemand (under Interactive Apps)
GipsyX	`module`	TBD	TBD
GMT	`module add gmt`	https://www.generic-mapping-tools.org/	GMT is an open-source collection of command-line tools for manipulating geographic and Cartesian data sets (including filtering, trend fitting, gridding, projecting, etc.) and producing high-quality illustrations ranging from simple x–y plots via contour maps to artificially illuminated surfaces and 3D perspective views
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
ISLE	-	http://stat.cmu.edu/isle/	A browser-based interactive statistics & data analysis platform. http://isle.hpc.tcnj.edu/
JDK	`module add jdk`	-	Java. Note: OpenJDK is recommended over this version (Oracle Java) due to licensing issues.
JDK/OpenJDK	`module add jdk/13`	https://openjdk.java.net/	OpenJDK. This overrides the built-in, older version provided with the OS.
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
Jupyter Notebook	-	https://jupyter-notebook.readthedocs.io/en/stable/notebook.html	Open-source web application that allows you to create and share documents that contain live code, equations, visualizations and narrative text. Web interface accessed via Open OnDemand (under Interactive Apps)
LAMMPS	`module add lammps`	https://lammps.sandia.gov/doc/Manual.html	Molecular dynamics simulator
mafft	`module add mafft`	https://mafft.cbrc.jp/alignment/software/	MAFFT is a program used to create multiple sequence alignments of amino acid or nucleotide sequences
Mathematica	`module add mathematica`	https://reference.wolfram.com/language/?source=nav	Single integrated, continually expanding system that covers the breadth and depth of technical computing. GUI accessed via Open OnDemand (under Interactive Apps)
Matlab	`module add matlab`	https://www.mathworks.com/help/	Desktop environment tuned for iterative analysis and design processes with a programming language that expresses matrix and array. GUI accessed via Open OnDemand (under Interactive Apps) mathematics directly
MGLtools	`module`	TBD	TBD
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
MPSolve	`module add mpsolve`	https://numpi.dm.unipi.it/software/mpsolve	MPSolve stands for Multiprecision Polynomial SOLVEr. It is a software that aims to provide an easy to use (hopefully) universal blackbox for solving polynomials and secular equations.
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
MSconvert	`module`	TBD	TBD
MUSCLE	`module add muscle`	https://www.drive5.com/muscle/manual/	MUSCLE is one of the best-performing multiple alignment programs according to published benchmark tests, with accuracy and speed that are consistently better than CLUSTALW
NAMD	`module add namd`	https://www.ks.uiuc.edu/Research/namd/	NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems
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
OpenMM	`module`	TBD	TBD
OpenMS	`module`	TBD	TBD
Open OnDemand	http://ondemand.hpc.tcnj.edu	Getting started with TCNJ ELSA HPC Open OnDemand	NSF-funded open-source HPC portal based on OSC’s original OnDemand portal. The goal of Open OnDemand is to provide an easy way for system administrators to provide web access to their HPC resources
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)
Partitionfinder	`module`	TBD	TBD
PAUP	`module`	TBD	TBD
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
Pride PPP-AR	`module`	TBD	TBD
PRINSEQ	`module add prinseq`	http://prinseq.sourceforge.net/manual.html	Filter, reformat, or trim your genomic and metagenomic sequence data
PWiz	`module`	TBD	TBD
Pylith	`module`	TBD	TBD
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
RAxML	`module add raxml`	https://cme.h-its.org/exelixis/web/software/raxml/index.html	RAxML (Randomized Axelerated Maximum Likelihood) is a program for sequential and parallelMaximum Likelihood based inference of large phylogenetic trees
RStudio Server	-	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`	https://sop-gpu.readthedocs.io/en/latest/	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
Torchvision	`module add python-vision`	https://github.com/pytorch/vision	The Torchvision package consists of popular datasets, model architectures, and common image transformations for computer vision
Transcriptomics	`module add transcriptomics`	bowtie2 - http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml fastqc - https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/ hisat - http://www.ccb.jhu.edu/software/hisat/manual.shtml hisat2 - https://ccb.jhu.edu/software/hisat2/manual.shtml samtools/bcftools - http://www.htslib.org/doc/ STAR - https://github.com/alexdobin/STAR/tree/master/doc stringtie - https://ccb.jhu.edu/software/stringtie/index.shtml?t=manual tophat - https://ccb.jhu.edu/software/tophat/manual.shtml	Various tools to support transcriptomics
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. Includes POV-Ray

@@ Line 1: / Line 1: @@
+The ELSA HPC cluster utilizes the [https://lmod.readthedocs.io/en/latest/ Lmod] environment module system. Lmod allows you to load and unload various environments to support multiple applications. It also allows you to select among different versions of an application depending on your requirements, e.g. load a Python 2.7.12 environment for application "A" and then load a Python 3.6.0 environment for application "B."
+When working interactively at the Linux command-line (e.g. on a login node or dev node), you can run the <code>module add ''module_name''</code> at the shell prompt to load a particular environment. You should also include the appropriate <code>module add ''module_name''</code> command(s) in your SLURM submission script. Use the <code>module avail</code> command at the Linux shell prompt to list all available modules. If you do not specify the version number when adding a module, it will usually load the newest version unless otherwise noted, e.g. <code>module add python</code> is equivalent to <code>module add python/3.6.0</code>.
+For more information on working with Lmod modules on the ELSA cluster see the dedicated [[HPC_Cluster_Lmod|ELSA Lmod tutorial]] page.
+'''Note: This software listing may be incomplete or contain software that is no longer available. It will be updated in the future. Use the''' <code>module avail</code> '''command to get the most updated list of available software packages.'''
 {| class="wikitable"
 |-
 ! width="10%" | Application Name !! width="17%" | Module Command !! width="30%" | Application Website/Docs !! width="43%" | Notes
+|-
+| ABySS|| <code>module add abyss</code> || https://docs.anaconda.com/anaconda/ || ABySS is a de novo sequence assembler intended for short paired-end reads and large genomes
+|-
+| Alphafold2 || <code>module</code> || TBD || TBD
 |-
 | Amber || <code>module add amber</code> || http://ambermd.org/Manuals.php || Amber is a suite of biomolecular simulation programs
+|-
+| anaconda || <code>module add anaconda3</code> || https://docs.anaconda.com/anaconda/ || Anaconda is a package manager, an environment manager, a Python/R data science distribution, and a collection of over 7,500+ open-source packages
+|-
+| ASTRAL|| <code>module add astral</code> || https://github.com/smirarab/ASTRAL/blob/master/astral-tutorial.md || ASTRAL is a java program for estimating a species tree given a set of unrooted gene trees
 |-
 | Athena || <code>module add athena</code> || https://princetonuniversity.github.io/Athena-Cversion/ || Athena is a grid-based code for astrophysical magnetohydrodynamics (MHD)
 |-
 | Athena++ || <code>module add athena++</code> || https://princetonuniversity.github.io/athena/ || Athena++ is a complete re-write of the Athena astrophysical magnetohydrodynamics (MHD) code in C++
+|-
+| Autodock Vina || <code>module</code> || TBD || TBD
 |-
 | Blast+ || <code>module add blast+</code> || https://www.ncbi.nlm.nih.gov/books/NBK279690/ || Basic Local Alignment Search Tool
+|-
+| Blender || <code>module</code> || TBD || TBD
 |-
 | Cassandra || <code>module add cassandra</code> || https://cassandra.nd.edu/index.php/documentation || Cassandra is an open source Monte Carlo package
 |-
-| <br>cuda/8.0<br>cuda/9.2<br>cuda/10.0 || <code>module add cuda</code><br><code>module add cuda/8.0</code><br><code>module add cuda/9.2</code><br><code>module add cuda/10.0</code> || https://docs.nvidia.com/cuda/ || Default is CUDA 9.2 if using <code>module add cuda</code>
+| ChimeraX || <code>module</code> || TBD || TBD
 |-
-| cuDNN || <code>module add cudnn</code> || https://docs.nvidia.com/deeplearning/sdk/cudnn-developer-guide/index.html || -
+| CIAO || <code>module</code> || TBD || TBD
+|-
+| CUDA || <code>module add cuda</code><br><code>module add cuda/8.0</code><br><code>module add cuda/10.1</code><br><code>module add cuda/10.2</code><br><code>module add cuda/11.4</code><br><code>module add cuda/11.7</code><br><code>module add cuda/11.8</code> || https://docs.nvidia.com/cuda/ || Default is CUDA 11.4 if using <code>module add cuda</code><p>CUDA 11.8 contains TensorRT 8.6.1.6 and cuDNN 8.9.5.29
+|-
+| ddcMD|| <code>module add ddcmd</code> || https://github.com/LLNL/ddcMD || A fully GPU-accelerated molecular dynamics program for the Martini force field
 |-
 | ELSA Tutorial || <code>module add elsa-tutorial</code> || TBA || Used with ELSA SLURM tutorial
 |-
 | ESPResSo || <code>module add espresso</code> || http://espressomd.org/wordpress/documentation/ || Extensible Simulation Package for Research on Soft Matter
+|-
+| FastQC || <code>module add fastqc</code> || TBD || TBD
 |-
 | FASTX-Toolkit || <code>module add fastx</code> || http://hannonlab.cshl.edu/fastx_toolkit/commandline.html || FASTQ/A short-reads pre-processing tools
@@ Line 32: / Line 56: @@
 |-
 | GaussView || - || http://gaussian.com/wp-content/uploads/dl/gv6.pdf || Graphical interface used with Gaussian which aids in the creation of Gaussian input files, enables the user to run Gaussian calculations from a graphical interface without the need for using a command line instruction, and helps in the interpretation of Gaussian output. GUI accessed via  [http://ondemand.hpc.tcnj.edu/ Open OnDemand] (under Interactive Apps)
+|-
+| GipsyX || <code>module</code> || TBD || TBD
+|-
+| GMT|| <code>module add gmt</code> || https://www.generic-mapping-tools.org/ || GMT is an open-source collection of command-line tools for manipulating geographic and Cartesian data sets (including filtering, trend fitting, gridding, projecting, etc.) and producing high-quality illustrations ranging from simple x–y plots via contour maps to artificially illuminated surfaces and 3D perspective views
 |-
 | GNUplot || <code>module add gnuplot</code> || http://www.gnuplot.info/documentation.html || Portable command-line driven graphing utility
@@ Line 41: / Line 69: @@
 | Hoomd-Blue || <code>module add hoomd-blue</code> || https://hoomd-blue.readthedocs.io/en/stable/ || General purpose particle simulation toolkit
 |-
-| JDK || <code>module add jdk</code> || - || 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.
+| ISLE || - || http://stat.cmu.edu/isle/ || A browser-based interactive statistics & data analysis platform. http://isle.hpc.tcnj.edu/
+|-
+| JDK || <code>module add jdk</code> || - || Java. Note: OpenJDK is recommended over this version (Oracle Java) due to licensing issues.
+|-
+| JDK/OpenJDK || <code>module add jdk/13</code> || https://openjdk.java.net/ || OpenJDK. This overrides the built-in, older version provided with the OS.
 |-
 | Jellyfish || <code>module add jellyfish</code> || http://www.genome.umd.edu/docs/JellyfishUserGuide.pdf || Fast, parallel k-mer counting for DNA
@@ Line 50: / Line 82: @@
 |-
 | LAMMPS || <code>module add lammps</code> || https://lammps.sandia.gov/doc/Manual.html || Molecular dynamics simulator
+|-
+| mafft|| <code>module add mafft</code> || https://mafft.cbrc.jp/alignment/software/ || MAFFT is a program used to create multiple sequence alignments of amino acid or nucleotide sequences
 |-
 | Mathematica || <code>module add mathematica</code> || https://reference.wolfram.com/language/?source=nav || Single integrated, continually expanding system that covers the breadth and depth of technical computing. GUI accessed via  [http://ondemand.hpc.tcnj.edu/ Open OnDemand] (under Interactive Apps)
 |-
 | Matlab || <code>module add matlab</code> || https://www.mathworks.com/help/ || Desktop environment tuned for iterative analysis and design processes with a programming language that expresses matrix and array. GUI accessed via  [http://ondemand.hpc.tcnj.edu/ Open OnDemand] (under Interactive Apps) mathematics directly
+|-
+| MGLtools || <code>module</code> || TBD || TBD
 |-
 | MOPAC || <code>module add mopac</code> || http://openmopac.net/manual/ || General-purpose semiempirical molecular orbital package. Primarily used from within the WebMO (http://webmo.hpc.tcnj.edu) system
 |-
 | MPMC || <code>module add mpmc</code> || https://github.com/mpmccode/mpmc/wiki || Massively parallel monte carlo
+|-
+| MPSolve || <code>module add mpsolve</code> || https://numpi.dm.unipi.it/software/mpsolve || MPSolve stands for Multiprecision Polynomial SOLVEr. It is a software that aims to provide an easy to use (hopefully) universal blackbox for solving polynomials and secular equations.
 |-
 | MrBayes || <code>module add mrbayes</code> || http://nbisweden.github.io/MrBayes/manual.html || Program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models
+|-
+| MSconvert || <code>module</code> || TBD || TBD
+|-
+| MUSCLE|| <code>module add muscle</code> || https://www.drive5.com/muscle/manual/ || MUSCLE is one of the best-performing multiple alignment programs according to published benchmark tests, with accuracy and speed that are consistently better than CLUSTALW
+|-
+| NAMD|| <code>module add namd</code> || https://www.ks.uiuc.edu/Research/namd/ || NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems
 |-
 | NetPBM || <code>module add netpbm</code> || http://netpbm.sourceforge.net/doc/ || Toolkit for manipulation of graphic images, including conversion of images between a variety of different formats
@@ Line 66: / Line 110: @@
 |-
 | Omnia || <code>module add omnia</code> || https://github.com/omnia-md/omnia-md || High performance, high usability toolkits for  predictive biomolecular simulation
+|-
+| OpenMM || <code>module</code> || TBD || TBD
+|-
+| OpenMS || <code>module</code> || TBD || TBD
 |-
 | Open OnDemand || http://ondemand.hpc.tcnj.edu || [http://docs.hpc.tcnj.edu/index.php/HPC_Cluster_Getting_Started#Open_OnDemand Getting started with TCNJ ELSA HPC Open OnDemand] || NSF-funded open-source HPC portal based on OSC’s original OnDemand portal. The goal of Open OnDemand is to provide an easy way for system administrators to provide web access to their HPC resources
 |-
 | ParaView || <code>module add paraview</code> || https://www.paraview.org/documentation/ || Open-source, multi-platform data analysis and visualization application. GUI accessed via  [http://ondemand.hpc.tcnj.edu/ Open OnDemand] (under Interactive Apps)
+|-
+| Partitionfinder || <code>module</code> || TBD || TBD
+|-
+| PAUP || <code>module</code> || TBD || TBD
 |-
 | pNetCDF || <code>module add pnetcdf</code> || 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
+|-
+| Pride PPP-AR || <code>module</code> || TBD || TBD
 |-
 | PRINSEQ || <code>module add prinseq</code> || http://prinseq.sourceforge.net/manual.html || Filter, reformat, or trim your genomic and metagenomic sequence data
+|-
+| PWiz || <code>module</code> || TBD || TBD
+|-
+| Pylith || <code>module</code> || TBD || TBD
 |-
 | Python || <code>module add python</code> || https://www.python.org/doc/ || Programming language that lets you work more quickly and integrate your systems more effectively
 |-
 | R || <code>module add R</code> || https://cran.r-project.org/manuals.html || Free software environment for statistical computing and graphics
+|-
+| RAxML || <code>module add raxml</code> || https://cme.h-its.org/exelixis/web/software/raxml/index.html || RAxML   (Randomized   Axelerated   Maximum   Likelihood)   is   a   program   for   sequential   and   parallelMaximum   Likelihood   based   inference   of   large   phylogenetic   trees
 |-
 | RStudio Server || - || https://resources.rstudio.com/ || Integrated development environment (IDE) for R. Web front-end accessed via [http://ondemand.hpc.tcnj.edu/ Open OnDemand] (under Interactive Apps)
@@ Line 97: / Line 157: @@
 | Swift || <code>module add swift</code> || http://swift-lang.org/docs/index.php || Simple tool for fast, easy scripting on big machines
 |-
-| Transcriptomics || <code>module add transcriptomics</code> || Example || Example
+| Torchvision || <code>module add python-vision</code> || https://github.com/pytorch/vision || The Torchvision package consists of popular datasets, model architectures, and common image transformations for computer vision
+|-
+| Transcriptomics || <code>module add transcriptomics</code> || bowtie2 - http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml<BR>fastqc - https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/<BR>hisat - http://www.ccb.jhu.edu/software/hisat/manual.shtml<BR>hisat2 - https://ccb.jhu.edu/software/hisat2/manual.shtml<BR>samtools/bcftools - http://www.htslib.org/doc/<BR>STAR - https://github.com/alexdobin/STAR/tree/master/doc<BR>stringtie - https://ccb.jhu.edu/software/stringtie/index.shtml?t=manual<BR>tophat - https://ccb.jhu.edu/software/tophat/manual.shtml || Various tools to support transcriptomics
 |-
 | 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
@@ Line 105: / Line 167: @@
 | 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> || 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
+| 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. Includes POV-Ray
 |}

HPC Cluster Software Resources: Difference between revisions

Latest revision as of 13:35, 29 May 2024

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