Software Installed on PSC Systems

This list includes software installed on Bridges-2 and Neocortex.  All Neocortex allocations include an allocation on Bridges-2 for general purpose computing.

For a list of all software installed on Bridges-2, type module spider. For a list of biological science software, type bioinformatics.

Anton 2 runs specific software written for its specialized hardware and is not included here.  See the Anton 2 documentation for specifics on Anton.

 

The module package on Bridges-2

The environment management package Module is essential for running software on Bridges-2. Be sure to check if there is a module for the software you want to use by typing module avail software-name.

To load the environment for a software package, which defines paths and variables needed to use the software, type module load software-name.

The module spider software-name command lists any additional modules that must also be loaded. Note that in some cases the order in which these additional modules are loaded matters. See documentation on the module command for more information.

 

Software Description Computing Resource
Abinit Calculates electronic density and derived properties of materials (incl. molecules, surfaces & solids) within DFT using pseudopotentials and a planewave or wavelet basis Bridges-2
ABySS Parallel assembler for short read sequence data Bridges-2
AI/ML/BD environments Prebuilt environments of AI/ML/BD packages
See also: Anaconda, Conda & Python documentation		 Bridges-2
AMBER Package of molecular simulation programs You must have your own license. PSC can help with installation.
Anaconda Open data science platform, includes popular Python, R and SCALA packages
See also AI environments, Conda, and Python documentation.		 Bridges-2
ANSYS General purpose finite element modeling package Bridges-2
AOCL Numerical library suite optimized for AMD processors Bridges-2
Arriba Detects gene fusions from RNA-Seq data Bridges-2
asciinema Allows recording and sharing terminal sessions Bridges-2
AUGUSTUS Predicts genes in eukaryotic genomic sequences Bridges-2
BAMTools C++ API and toolkit for analyzing and managing BAM files Bridges-2
BCFTools Utilities for variant calling and manipulating VCFs and BCFs Bridges-2
Bedops Tools to address common questions raised in genomics studies Bridges-2
Bedtools Utilities for comparing, summarizing and intersecting genomic features in the UCSC Genome Browser BED format Bridges-2
Bismark Bisulfite read mapper and methylation caller Bridges-2
BLAST Search tool that finds regions of local similarity between nucleotide or protein sequences Bridges-2
BLAT Alignment tool like BLAST, but structured differently Bridges-2
Boost Peer reviewed C++ source libraries Bridges-2
Bowtie2 Ultrafast, memory-efficient tool for aligning sequencing reads to long reference sequences. See related tool Bowtie. Bridges-2
BUSCO Assesses genome assembly and annotation completeness Bridges-2
BWA Fast light-weight tool that aligns relatively short sequences to a sequence database Bridges-2
C, C++
See the  Bridges-2 User Guide for documentation on C and C++		 Programming languages Bridges-2
Caffe Deep learning framework Bridges-2
CheckM Tools to assess the quality of genomes recovered from isolates, single cells, or metagenomes Bridges-2
Circos Displays data in a circular layout Bridges-2
CMake Tools to control the compilation process, build, test and package software Bridges-2
Conda Environment manager for all languages
See also AI environments, Anaconda, & Python documentation		 Bridges-2
CP2K Atomistic simulations of solid state, liquid, molecular, periodic, material, crystal, and biological systems Bridges-2
CUDA Parallel computing platform and API model Bridges-2
Cutadapt Reads a FASTA or FASTQ file, finds and removes adapters, writes the changed sequence to standard output Bridges-2
DDT Debugger for C, C++ and Fortran 90 threaded and parallel codes Bridges-2
deal.ii C++ library for finite element codes Bridges-2
Dorado High-performance, easy-to-use, open source basecaller for Oxford Nanopore reads Bridges-2
DReAMM Designs, renders and animates the output from a MCell simulation
FastANI Fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI) Bridges-2
FASTA-Splitter Divides a single FASTA file into multiple files Bridges-2
FASTQ-Splitter Divides a single FASTQ file into multiple files Bridges-2
FastQC Quality control tool for high throughput sequence data Bridges-2
FASTX Toolkit Command line tools for Short-Reads FASTA/FASTQ files preprocessing Bridges-2
FFTW3 C subroutine library for computing the DFT in one or more dimensions, of arbitrary input size, of both real and complex data Bridges-2
Filtlong Tool to filter long reads by quality Bridges-2
FLASh Fast and accurate tool to merge paired-end reads from NGS experiments Bridges-2
Fluent Computational fluid dynamics, part of ANSYS Bridges-2
Fortran
See the Bridges-2 User Guide for documentation on Fortran		 Programming language Bridges-2
Funannotate Genome prediction, annotation and comparison Bridges-2
GAMESS Ab initio molecular quantum chemistry Bridges-2
GATK Genome Analysis Toolkit, for high-throughput sequencing data Bridges-2
Gaussian Electronic structure program

Bridges-2

Access is restricted. You must complete the PSC Gaussian User Agreement to obtain access. See the GAUSSIAN document for details.
GCCSee theBridges-2 User Guide for documentation on the GNU compilers (GNU Compiler Collection) Compiler system supporting various programming languages Bridges-2
GeneMark-ES Gene prediction in eukaryotes Bridges-2
GeNT Computes the cross entropy for groups of sequences that have been assigned to groups on the basis of biochemical, physiological, or another biological property Bridges-2
Git Version control system for tracking changes in files and coordinating work on files among multiple people Bridges-2
GNU Parallel Shell tool for executing jobs in parallel using one or more computers Bridges-2
GROMACS Molecular dynamics software primarily designed for biomolecular systems Bridges-2
Guppy Data processing toolkit containing the Oxford Nanopore Technologies’ basecalling algorithms Bridges-2
Gurobi Mathematical programming solver

Bridges-2

Licensed for academic research use only. Researchers must submit the PSC Gurobi request form. See the Gurobi document for details.
hashdeep Computes hash files, or message digests, for any number of files Bridges-2
HDF5/PHDF5 Data model, library, and file format for storing and managing data and its parallel version Bridges-2
HISAT2 Fast, sensitive alignment, mapping NGS reads (DNA & RNA) to a population of human genomes or against a single reference genome Bridges-2
HMMER Biosequence analysis using profile hidden Markov models Bridges-2
Homer Suite of tools for motif discovery and next-gen sequence analysis Bridges-2
HPN-SSH Series of patches for OpenSSH to provide improved performance and functionality
HTSlib C library for reading and writing high-throughput sequence data Bridges-2
iCommands Library of commands to access iRODS servers Bridges-2
Infernal Searches DNA sequence databases for RNA structure and sequence similarities Bridges-2
ICC (Intel)See the  Bridges-2 User Guide for documentation on the Intel compilers Intel compilers, libraries and MPI implementation Bridges-2
Java Programming language Bridges-2
Julia High-level, high performance dynamic programming language for numerical computing Bridges-2
Jupyter Create and share code, visualizations, equations, more Bridges-2
Keras Minimalist, highly modular neural networks library written in Python and capable of running on top of either TensorFlow or Theano Bridges-2
Kracken2 Taxonomic sequence classifier that assigns taxonomic labels to DNA sequences Bridges-2
LAMMPS Classical molecular dynamics code Bridges-2
lazygit Simple terminal UI for git commands Bridges-2
lowcharts Tool to draw low-resolution charts in the terminal Bridges-2
LSMS Locally Self-consistent Multiple Scattering method, an order-N approach to the calculating the electronic structure of large systems within the local density approximation
MATLAB High-level language and interactive environment, performs computationally intensive tasks faster than traditional languages

Bridges-2

Academic users must complete the PSC MATLAB request form. Non-academic users should contact help@psc.edu.  See the MATLAB document for details.
MCell Monte Carlo Cell, simulates the movements and reactions of molecules within and between cells
MEME Suite Collection of tools for the discovery and analysis of sequence motifs Bridges-2
Methylpy Bisulfate sequencing data processing and differential methylation analysis Bridges-2
Minialign A little bit fast and moderately accurate nucleotide sequence alignment tool for PacBio & Nanopore long reads Bridges-2
MKL Math Kernel Library, highly optimized and threaded routines for linear algebra, FFTs, vector math and random number generators Bridges-2
MPI Message Passing Interface. Both Intel MPI and Open MPI are available.See the Bridges-2 User Guide for documentation on MPI. Bridges-2
MVAPICH Library exploiting novel features and mechanisms of high performance networking technologies. Delivers improved performance and scalability to MPI applications. Bridges-2
NAMD Parallel, object-oriented molecular dynamics code designed for high performance simulation of large biomolecular systems Bridges-2
Nanoplot Plotting tool for long read sequencing data and alignments Bridges-2
Ncdu Disk usage analyzer Bridges-2
ncview Viewer for netCDF format files Bridges-2
Nextflow DSL for parallel and scalable computational pipelines Bridges-2
NVHPCSee the  Bridges-2 User Guide for documentation on the NVHPC (formerly named PGI) compilers NVHPC (formerly called PGI) compilers and Tools Bridges-2
NWCHEM Computes the properties of molecular and periodic systems using standard quantum mechanical descriptions of the electronic wavefunction or density Bridges-2
Octave High-level programming language, intended for computation Bridges-2
OnDemand Web browser interface to manage files, submit and track jobs on Bridges-2 Bridges-2
OpenBLAS Optimized BLAS library Bridges-2
OpenCV Open source library of several hundred computer vision algorithms Bridges-2
OpenFOAM Finite volume CFD package Bridges-2
OpenMPI
See the Bridges-2 User Guide for documentation on OpenMPI		 High performance message passing library Bridges-2
ORCA Ab-initio quantum chemistry

Bridges-2

Before you can use ORCA on Bridges-2, you must register with ORCA and submit the PSC ORCA request form.  See the ORCA document for details.
Perl Programming language Bridges-2

PGI

See the  Bridges-2 User Guide for documentation on the PGI, now named NVHPC compilers

 NVHPC (formerly called PGI) compilers and Tools Bridges-2
PHYLIP Package for inferring phylogenies Bridges-2
Picard Java-based command-line utilities that manipulate SAM files, and a Java API (SAM-JDK) for creating new programs that read and write SAM files Bridges-2
PLUMED Library of enhanced sampling methods, free energy methods, tools to analyze data for MD simulations Bridges-2
Porechop Tool which finds and removes adapters from Oxford Nanopore reads Bridges-2
pnetCDF high performance, parallel library for files compatible with netCDF Bridges-2
Prodigal Open source lightweight microbial genefinding program Bridges-2
Prokka Software tool for rapid annotation of prokaryotic genomes Bridges-2
Python (including  numpy, scipy) Powerful, object-oriented programming language
See also AI environment, Conda and Anaconda documentation		 Bridges-2
PyTorch Machine Learning framework
See also AI environment documentation		 Bridges-2, Neocortex
Quantum Espresso Integrated suite of codes for electronic-structure calculations and materials modeling at the nanoscale Bridges-2
R Language and environment and an IDE for statistical computing and graphs Bridges-2
RAPIDS Framework bundling libraries to execute end-to-end data science pipelines on top of GPUs Bridges-2
RAxML Maximum likelihood phylogeny estimation for interpreting relationships between sets of data Bridges-2
Rclone Tool for managing files in cloud storage Bridges-2
RNAview Generates 2-dimensional displays of RNA/DNA secondary structures with tertiary interactions Bridges-2
SAMtools Utilities for manipulating alignments in SAM format Bridges-2
Scikit-learn Simple and efficient tools for data mining and data analysis, built on NumPy, SciPy and matplotlib Bridges-2
Siesta Performing efficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids Bridges-2
Singularity Open-source software container platform Bridges-2
SPAdes St. Petersburg genome assembler – an assembly toolkit with various assembly pipelines Bridges-2
Spark Open source software web application framework and domain-specific language written in Java Bridges-2
SRA toolkit Collection of tools and libraries for using data in the INSDC Sequence Read Archives Bridges-2
STAR-Fusion Uses the STAR aligner to identify candidate fusion transcripts supported by Illumina reads, maps junction and spanning reads to a reference annotation set Bridges-2
STAR Aligner Spliced Transcripts Alignment to Reference, an alignment tool for RNA sequences Bridges-2
TensorFlow Machine learning library for numerical computation using data flow graphs
See also AI environment documentation		 Bridges-2, Neocortex
Theano Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently Bridges-2
TIGER Precisely maps IGEs in bacterial and archaeal genomes Bridges-2
tmux Terminal multiplexer; create and control multiple terminals Bridges-2
Trinity Package which enables the efficient and robust de novo reconstruction of transcriptomes from RNA-Seq data Bridges-2
tRNAscan-se Program for improved detection of transfer RNA genes in genomic sequence Bridges-2
VASP Atomic scale materials modeling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics, from first principles You must have your own license. PSC can help with installation.
VCF2MAF Tool to convert VCFs to MAFs Bridges-2
VCFtools Tool providing easily accessible methods for working with complex genetic variation data in the form of VCF files Bridges-2
VisiData Interactive tool to manage tabula data Bridges-2
Visit Interactive and scalable visualization, animation and analysis tool Bridges-2
VTune Performance analysis tool for serial, multithreaded or MPI applications Bridges-2
WIEN2k Electronic structure calculations of solids using DFT You must have your own license. PSC can help with installation.
Xfig and transfig Interactive drawing tools Bridges-2
Zoltan Data management services for unstructured, adaptive and dynamic applications Bridges-2