Software installed 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:

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

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 Computing Resource
Anaconda Open data science platform, includes popular Python, R and SCALA packages Bridges-2
ANSYS General purpose finite element modeling package Bridges-2
Aspera Allows for rapid transfer of large files and data sets Bridges-2
ATLAS ANSI C and Fortran77 interfaces for the entire BLAS API, and a some of the LAPACK AP 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
Bowtie Ultrafast, memory-efficient short read aligner. See related tool Bowtie2. Bridges-2
Bowtie2 Ultrafast, memory-efficient tool for aligning sequencing reads to long reference sequences. See related tool Bowtie. Bridges-2
BWA Fast light-weight tool that aligns relatively short sequences to a sequence database Bridges-2
C, C++ Programming languages Bridges-2
Caffe Deep learning framework Bridges-2
CMake Tools to control the compilation process, build, test and package software 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
Eigen C++ template library for linear algebra: matrices, vectors, numerical solvers and related algorithms 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
Fluent Computational fluid dynamics, part of ANSYS Bridges-2
Fortran Programming language Bridges-2
Galaxy Open, web-based platform for data intensive biomedical research.  Bridges-2
GATK Genome Analysis Toolkit, for high-throughput sequencing data Bridges-2
Gaussian Electronic structure program Bridges-2
GCC (GNU Compiler Collection) Compiler system supporting various programming languages Bridges-2
GDAL Geospatial Data Abstraction Library 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
Gurobi Mathematical programming solver Bridges-2
Hadoop Big Data processing framework 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
ICC Intel compilers, libraries and MPI implementation Bridges-2
Java Programming language Bridges-2
JPEG Method of lossy compression for digital images 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
LAMMPS Classical molecular dynamics code Bridges-2
LevelDB Fast key-value storage library that provides an ordered mapping from string keys to string values. Bridges-2
MATLAB High-level language and interactive environment, performs computationally intensive tasks faster than traditional languages Bridges-2
Maven Apache build manager for Java projects Bridges-2
MetaPhlAn/ MetaPhlAn 2 Computational tools for profiling the composition of microbial communities from metagenomic shotgun sequencing data Bridges-2
MPI Message Passing Interface. Both Intel MPI and Open MPI are available. Bridges-2
MuST ab initio electronic structure calculation Bridges-2
NAMD Parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems Bridges-2
NetCDF Software libraries and self-describing, machine-independent data formats supporting the creation, access, and sharing of array-oriented scientific data Bridges-2
NWCHEM Computes the properties of molecular and periodic systems using standard quantum mechanical descriptions of the electronic wavefunction or density Bridges-2
OnDemand Web browser interface to manage files, submit and track jobs on Briges Bridges-2
OpenBLAS Optimized BLAS library Bridges-2
OpenCV Open source library of several hundred computer vision algorithms Bridges-2
OpenMPI High performance message passing library Bridges-2
Perl Programming language Bridges-2
PGI PGI compilers and Tools 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
Prodigal Open source lightweight microbial genefinding program Bridges-2
Protocol buffer Protocol Buffers, method of serializing structured data Bridges-2
Python (including  matplotlib, numpy, scipy) Powerful, object-oriented programming language Bridges-2
Quantum Espresso Integrated suite of codes for electronic-structure calculations and materials modeling at the nanoscale Bridges-2
R, RStudio (including the ggplot2 package) Language and environment and an IDE for statistical computing and graphs Bridges-2
RAxML Maximum likelihood phylogeny estimation for interpreting relationships between sets of data Bridges-2
SAMtools Utilities for manipulating alignments in SAM format 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 dentify 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
TAU Tuning and Analysis Utilities Bridges-2
TensorFlow Machine learning library for numerical computation using data flow graphs 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
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 Bridges-2
WIEN2k Electronic structure calculations of solids using DFT You must have your own license. PSC can help with installation.
Zlib Data compression library Bridges-2
Zoltan Data management services for unstructured, adaptive and dynamic applications Bridges-2

Important dates for 2020

Next research allocation submission dates Sept. 15 - Oct. 15
Early User Program Fall
Production operations begin Fall

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