Software on Bridges-2
This is an initial list of software to be installed on Bridges-2 for the Early User Program. Additional applications may be installed as requested. You can request software by using this form: https://psc.edu/bridges-2/software-request.
The Module package
The environment management package Module is essential for running software on most PSC systems. Be sure to check if there is a module for the software you want to use by typing
module avail software-name
More infomation about the software and their modules is available by typing
module spider 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 help 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 | |
| ABySS | Parallel assembler for short read sequence data | |
| Anaconda | Open data science platform, includes popular Python, R and SCALA packages | |
| ANSYS | General purpose finite element modeling package | |
| AOCC | AMD compilers for use on the RM nodes | |
| Aspera | Allows for rapid transfer of large files and data sets | |
| ATLAS | ANSI C and Fortran77 interfaces for the entire BLAS API, and a some of the LAPACK AP | |
| BAMTools | C++ API and toolkit for analyzing and managing BAM files | |
| BCFTools | Utilities for variant calling and manipulating VCFs and BCFs | |
| BEDOPS | Tools to address common questions raised in genomics studies | |
| Bedtools | Utilities for comparing, summarizing and intersecting genomic features in the UCSC Genome Browser BED format | |
| Bismark | Bisulfite read mapper and methylation caller | |
| BLAST | Search tool that finds regions of local similarity between nucleotide or protein sequences | |
| BLAT | Alignment tool like BLAST, but structured differently | |
| Boost | Peer reviewed C++ source libraries | |
| Bowtie | Ultrafast, memory-efficient short read aligner. See related tool Bowtie2. | |
| Bowtie2 | Ultrafast, memory-efficient tool for aligning sequencing reads to long reference sequences. See related tool Bowtie. | |
| BWA | Fast light-weight tool that aligns relatively short sequences to a sequence database | |
| C, C++ | Programming languages | |
| Caffe | Deep learning framework | |
| CMake | Tools to control the compilation process, build, test and package software | |
| CP2K | Atomistic simulations of solid state, liquid, molecular, periodic, material, crystal, and biological systems | |
| CUDA | Parallel computing platform and API model | |
| Cutadapt | Reads a FASTA or FASTQ file, finds and removes adapters, writes the changed sequence to standard output | |
| DDT | Debugger for C, C++ and Fortran 90 threaded and parallel codes | |
| Eigen | C++ template library for linear algebra: matrices, vectors, numerical solvers and related algorithms | |
| FastQC | Quality control tool for high throughput sequence data | |
| FASTX Toolkit | Tools for preprocessing data from FASTA and FASTQ files | |
| FFTW3 | C subroutine library for computing the DFT in one or more dimensions, of arbitrary input size, of both real and complex data | |
| FLASh | Fast and accurate tool to merge paired-end reads from NGS experiments | |
| Fortran | Programming language | |
| Galaxy | Open, web-based platform for data intensive biomedical research. | |
| GATK | Genome Analysis Toolkit, for high-throughput sequencing data | |
| Gaussian | Electronic structure program | |
| GCC | (GNU Compiler Collection) Compiler system supporting various programming languages | |
| GDAL | Geospatial Data Abstraction Library | |
| GNU Parallel | Shell tool for executing jobs in parallel using one or more computers | |
| GROMACS | Molecular dynamics software primarily designed for biomolecular systems | |
| Gurobi | Mathematical programming solver | |
| Hadoop | Big Data processing framework | |
| HDF5/PHDF5 | Data model, library, and file format for storing and managing data and its parallel version | |
| HISAT2 | Fast, sensitive alignment, mapping NGS reads (DNA & RNA) to a population of human genomes or against a single reference genome | |
| HMMER | Biosequence analysis using profile hidden Markov models | |
| Homer | Suite of tools for motif discovery and next-gen sequence analysis | |
| Intel | Intel compilers, libraries and MPI implementation | |
| Java | Programming language | |
| JPEG | Method of lossy compression for digital images | |
| Julia | High-level, high-performance dynamic programming language for numerical computing | Bridges |
| Keras | Minimalist, highly modular neural networks library written in Python and capable of running on top of either TensorFlow or Theano | |
| LAMMPS | Classical molecular dynamics code | |
| LevelDB | Fast key-value storage library that provides an ordered mapping from string keys to string values. | |
| MATLAB | High-level language and interactive environment, performs computationally intensive tasks faster than traditional languages | |
| Maven | Apache build manager for Java projects | |
| MetaPhlAn/ MetaPhlAn 2 | Computational tools for profiling the composition of microbial communities from metagenomic shotgun sequencing data | |
| MKL | Math Kernel Library, highly optimized and threaded routines for linear algebra, FFTs, vector math and random number generators | |
| MPI | Message Passing Interface. Both Intel MPI and Open MPI are available. | |
| MuST | ab initio electronic structure calculation | |
| NAMD | Parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems | |
| NWCHEM | Computes the properties of molecular and periodic systems using standard quantum mechanical descriptions of the electronic wavefunction or density | |
| OnDemand | Web browser interface to manage files, submit and track jobs on Briges | |
| OpenBLAS | Optimized BLAS library | |
| OpenCV | Open source library of several hundred computer vision algorithms | |
| OpenMPI | High performance message passing library | |
| Perl | Programming language | |
| PGI | PGI compilers and Tools | |
| 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 | |
| pnetCDF | High-performance, parallel library for files compatible with netCDF | |
| Prodigal | Open source lightweight microbial genefinding program | |
| Protocol buffer | Protocol Buffers, method of serializing structured data | |
| Python (including matplotlib, numpy, scipy) | Powerful, object-oriented programming language | |
| Quantum Espresso | Integrated suite of codes for electronic-structure calculations and materials modeling at the nanoscale | |
| R, RStudio (including the ggplot2 package) | Language and environment and an IDE for statistical computing and graphs | |
| RAxML | Maximum likelihood phylogeny estimation for interpreting relationships between sets of data | |
| SAMtools | Utilities for manipulating alignments in SAM format | |
| Singularity | Open-source software container platform | |
| SPAdes | St. Petersburg genome assembler – an assembly toolkit with various assembly pipelines | |
| Spark | Open source software web application framework and domain-specific language written in Java | |
| SRA toolkit | Collection of tools and libraries for using data in the INSDC Sequence Read Archives | |
| STAR-Fusion | Uses the STAR aligner to dentify candidate fusion transcripts supported by Illumina reads, maps junction and spanning reads to a reference annotation set | |
| STAR Aligner | Spliced Transcripts Alignment to Reference, an alignment tool for RNA sequences | |
| TAU | Tuning and Analysis Utilities | |
| TensorFlow | Machine learning library for numerical computation using data flow graphs | |
| tmux | Terminal multiplexer; create and control multiple terminals | |
| Trinity | Package which enables the efficient and robust de novo reconstruction of transcriptomes from RNA-Seq data | |
| VASP |
Atomic scale materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics, from first principles. You must have your own license. PSC can help with installation. |
|
| VCFtools | Tool providing easily accessible methods for working with complex genetic variation data in the form of VCF files | |
| WIEN2k |
Electronic structure calculations of solids using DFT You must have your own license. PSC can help with installation. |
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| Zlib | Data compression library | |
| Zoltan | Data management services for unstructured, adaptive and dynamic applications |