---------------------------------------------------------------------------- The following is a list of the modules currently available: ---------------------------------------------------------------------------- ABINIT: ABINIT/8.0.8b-GCC-4.9.2, ABINIT/8.0.8b-GCC-4.9.3, ... ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave or wavelet basis. ABRicate: ABRicate/0.8.7-spartan_intel-2017.u2 Mass screening of contigs for antimicrobial resistance or virulence genes. It comes bundled with multiple databases: Resfinder, CARD, ARG-ANNOT, NCBI BARRGD, NCBI, EcOH, PlasmidFinder, Ecoli_VF and VFDB. ABySS: ABySS/1.5.2-goolf-2015a, ABySS/1.9.0-goolf-2015a, ... Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler - Homepage: http://www.bcgsc.ca/platform/bioinfo/software/abyss ACTC: ACTC/1.1-intel-2016.u3 ACTC converts independent triangles into triangle strips or fans. - Homepage: https://sourceforge.net/projects/actc ADMIXTURE: ADMIXTURE/1.3.0 ADMIXTURE is a software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets. It uses the same statistical model as STRUCTURE but calculates estimates much more rapidly using a fast numerical optimization algorithm. - Homepage: https://www.genetics.ucla.edu/software/admixture AFNI: AFNI/linux_openmp_64-intel-2016.u3-20180104, ... Free software for analysis and display of FMRI data ANSYS_CFD: ANSYS_CFD/18.1, ANSYS_CFD/19.0 ANSYS computational fluid dynamics (CFD) simulation software allows you to predict, with confidence, the impact of fluid flows on your product throughout design and manufacturing as well as during end use. ANSYS renowned CFD analysis tools include the widely used and well-validated ANSYS Fluent and ANSYS CFX. ANTLR: ANTLR/2.7.7-intel-2016.u3, ANTLR/2.7.7-intel-2017.u2 ANTLR, ANother Tool for Language Recognition, (formerly PCCTS) is a language tool that provides a framework for constructing recognizers, compilers, and translators from grammatical descriptions containing Java, C#, C++, or Python actions. ANTs: ANTs/2.2.0-goolf-2015a, ANTs/2.2.0-intel-2016.u3, ... ANTs extracts information from complex datasets that include imaging. ANTs is useful for managing, interpreting and visualizing multidimensional data. APR: APR/1.5.2-GCC-4.9.2 Apache Portable Runtime (APR) libraries. - Homepage: http://apr.apache.org/ APR-util: APR-util/1.5.4-GCC-4.9.2 Apache Portable Runtime (APR) util libraries. - Homepage: http://apr.apache.org/ ARAGORN: ARAGORN/1.2.36-GCC-4.9.2 ATK: ATK/2.18.0-intel-2016.u3, ATK/2.24.0-GCC-4.9.2, ATK/2.24.0-GCC-6.2.0, ... ATK provides the set of accessibility interfaces that are implemented by other toolkits and applications. Using the ATK interfaces, accessibility tools have full access to view and control running applications. - Homepage: https://developer.gnome.org/ATK/stable/ ATLAS: ATLAS/3.10.1-GCC-4.9.2-LAPACK-3.5.0, ... ATLAS (Automatically Tuned Linear Algebra Software) is the application of the AEOS (Automated Empirical Optimization of Software) paradigm, with the present emphasis on the Basic Linear Algebra Subprograms (BLAS), a widely used, performance-critical, linear algebra kernel library. - Homepage: http://math-atlas.sourceforge.net ATSAS: ATSAS/2.8.0-2.el7.x86_64 ATSAS is a program suite for small-angle scattering data analysis from biological macromolecules. - Homepage: http://www.embl-hamburg.de/ExternalInfo/Research/Sax/software.html AUGUSTUS: AUGUSTUS/3.2.3-intel-2017.u2-Python-2.7.13, ... AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences Albacore: Albacore/2.3.3-intel-2017.u2-Python-3.6.4 Albacore identifies DNA sequences directly from raw data, rather than utilising an intermediary stage called ‘event detection’. This upgrade enhances accuracy of the single-read sequence data, contributing to high consensus accuracy for nanopore sequence data. AlignGraph: AlignGraph/20160823-intel-2016.u3 Amber: Amber/16-GCC-6.2.0-CUDA, Amber/16-GCC-6.2.0, ... Amber (originally Assisted Model Building with Energy Refinement) is software for performing molecular dynamics and structure prediction. AmberTools: AmberTools/18-spartan_intel-2017.u2 AmberTools consists of several independently developed packages that work well by themselves, and with Amber itself. The suite can also be used to carry out complete molecular dynamics simulations, with either explicit water or generalized Born solvent models. Anaconda2: Anaconda2/4.2.0 Anaconda is the leading open data science platform powered by Python. The open source version of Anaconda is a high performance distribution of Python and R and includes over 100 of the most popular Python, R and Scala packages for data science. Anaconda3: Anaconda3/5.0.1, Anaconda3/5.1.0, Anaconda3/5.3.0, ... Built to complement the rich, open source Python community, the Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture. Armadillo: Armadillo/6.600.4-intel-2016.u3-Python-2.7.10, ... Armadillo is an open-source C++ linear algebra library (matrix maths) aiming towards a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, as well as a subset of trigonometric and statistics functions. Array-Utils: Array-Utils/0.5-intel-2016.u3 small utils for array manipulation Aspera-Connect: Aspera-Connect/3.6.1 Connect is an install-on-demand Web browser plug-in that facilitates high-speed uploads and downloads with an Aspera transfer server. Autoconf: Autoconf/2.69-foss-2017b, Autoconf/2.69-GCC-4.6.4, ... Automake: Automake/1.11-GCC-4.9.2, Automake/1.14-GCC-4.9.2, ... Autotools: Autotools/20150119-foss-2017b, Autotools/20150119-GCC-4.6.4, ... This bundle collect the standard GNU build tools: Autoconf, Automake and libtool - Homepage: http://autotools.io BAMM: BAMM/2.5.0-spartan_intel-2017.u2 BAMM is oriented entirely towards detecting and quantifying heterogeneity in evolutionary rates. It uses reversible jump Markov chain Monte Carlo to automatically explore a vast universe of candidate models of lineage diversification and trait evolution. BBMap: BBMap/36.62-intel-2016.u3-Java-1.8.0_71, BBMap/37.68, BBMap/37.93, ... BBMap short read aligner, and other bioinformatic tools. - Homepage: https://sourceforge.net/projects/bbmap/ BCFtools: BCFtools/1.2-intel-2016.u3, BCFtools/1.3-intel-2016.u3, ... Samtools is a suite of programs for interacting with high-throughput sequencing data. BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants BEDTools: BEDTools/2.25.0-intel-2016.u3, BEDTools/2.26.0-intel-2016.u3, ... BLACS: BLACS/1.1-goolf-2015a, BLACS/1.1-intel-2017.u2 The BLACS (Basic Linear Algebra Communication Subprograms) project is an ongoing investigation whose purpose is to create a linear algebra oriented message passing interface that may be implemented efficiently and uniformly across a large range of distributed memory platforms. - Homepage: http://www.netlib.org/blacs/ BLAST: BLAST/2.2.26-Linux_x86_64 BLAST+: BLAST+/2.7.1-GCC-6.2.0-Python-3.5.2, BLAST+/2.7.1-intel-2016.u3, ... Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences. BLAT: BLAT/3.5-intel-2016.u3 BLIS: BLIS/0.5.1-GCC-6.2.0-Python-2.7.13, ... BWA: BWA/0.6.2-GCC-4.9.2, BWA/0.6.2-intel-2016.u3, ... BamTools: BamTools/2.3.0-intel-2016.u3, BamTools/2.4.0-intel-2016.u3, ... Barrnap: Barrnap/0.6-intel-2016.u3 Barrnap predicts the location of ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S). Bazel: Bazel/0.8.0, Bazel/0.11.0-GCC-6.4.0 Bazel is a build tool that builds code quickly and reliably. It is used to build the majority of Google's software. Beast: Beast/1.8.3-intel-2016.u3, Beast/1.8.3, ... BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. Bicycle: Bicycle/1.8.1-intel-2018.u4-Java-9.0.4 bicycle (bisulfite-based methylcytosine caller) is a next-generation sequencing bioinformatic pipeline aimed to analyze whole genome bisulfite sequencing data. It can process data from directional (Lister) and non-directional (Cokus) bisulfite sequencing protocols, and from single-end and paired-end sequencing, and performs methylation calls for cytosines in CG and non-CG contexts (CHG and CHH). BioPerl: BioPerl/1.6.924-intel-2016.u3-Perl-5.20.0-bio, ... Bioperl is the product of a community effort to produce Perl code which is useful in biology. Examples include Sequence objects, Alignment objects and database searching objects. Biopython: Biopython/1.61-intel-2016.u3-Python-2.7.10, ... Biopython is a set of freely available tools for biological computation written in Python by an international team of developers. It is a distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics. Bismark: Bismark/0.20.0-intel-2016.u3 A tool to map bisulfite converted sequence reads and determine cytosine methylation states Bison: Bison/2.7-GCC-4.9.2, Bison/2.7-intel-2016.u3, Bison/2.7, ... Blender: Blender/2.77a-intel-2016.u3-Python-3.5.2, ... Blender is the free and open source 3D creation suite. It supports the entirety of the 3D pipeline-modeling, rigging, animation, simulation, rendering, compositing and motion tracking, even video editing and game creation. - Homepage: https://www.blender.org/ Blosc: Blosc/1.12.1-intel-2017.u2 Blosc, an extremely fast, multi-threaded, meta-compressor library Boost: Boost/1.46.1-goolf-2015a, Boost/1.54.0-GCC-4.9.2-Python-2.7.9, ... Boost provides free peer-reviewed portable C++ source libraries. Bowtie: Bowtie/1.2.1.1-intel-2017.u2, Bowtie/1.2.1.1 Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB for paired-end). Bowtie2: Bowtie2/2.1.0-intel-2016.u3, Bowtie2/2.2.5-GCC-4.9.2, ... Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes. Bracken: Bracken/1.0.0, Bracken/2.2.0 Bracken: estimating species abundance in metagenomics data CAT: CAT/06092016-intel-2016.u3 CD-HIT: CD-HIT/4.6.1-intel-2016.u3-2012-08-27, CD-HIT/4.6.8-foss-2017b, ... CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences. CESM: CESM/1.0.6 CGAL: CGAL/4.7-intel-2016.u3-Python-2.7.9, ... The goal of the CGAL Open Source Project is to provide easy access to efficient and reliable geometric algorithms in the form of a C++ library. CIRI: CIRI/2.0.6-intel-2018.u4-Perl-5.26.2 CircRNA Identifier. A de novo circular RNA identification tool CLCWorkbench: CLCWorkbench/8.0.1_64 CLC Main Workbench is used by tens of thousands of researchers all over the world for DNA, RNA, and protein sequence data analysis. Its wide variety of features are presented in an intuitive graphical user-interface, for which advanced computer skills are not required. CLISP: CLISP/2.49-GCC-6.2.0, CLISP/2.49-GCCcore-6.4.0 Common Lisp is a high-level, general-purpose, object-oriented, dynamic, functional programming language. CMake: CMake/2.8.4-intel-2016.u3, CMake/2.8.12-GCC-4.9.2, ... CNTKCustomMKL: CNTKCustomMKL/3 This is a custom version of Intel's Math Kernel Library for Microsoft's Cognitive Toolkit, packaged by the CNTK team. I have no idea why Microsoft keeps doing things like this, their ostensible reasoning is that this means users don't need access to the (now freely available) Intel MKL. Ok. --Dan - Homepage: https://github.com/Microsoft/CNTK/ COMSOL: COMSOL/5.2, COMSOL/5.3a, COMSOL/5.4 COMSOL is a cross-platform finite element analysis, solver and multipyhsics simulation software CPLEX: CPLEX/12.7.1, CPLEX/12.8, CPLEX/12.63 CRISPR: CRISPR/1.2-Java-1.8.0_152 CRISPR Recognition Tool CUDA: CUDA/7.0.28-GCC-4.9.2, CUDA/7.0.28-intel-2016.u3, CUDA/7.0.28, ... CUDA (formerly Compute Unified Device Architecture) is a parallel computing platform and programming model created by NVIDIA and implemented by the graphics processing units (GPUs) that they produce. CUDA gives developers access to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs. Caffe: Caffe/20171110-intel-2017.u2-GCC-5.4.0-CUDA8 Caffe is a deep learning framework made with expression, speed, and modularity in mind. It is developed by the Berkeley Vision and Learning Center (BVLC) and by community contributors. Canu: Canu/1.3-GCC-4.9.3, Canu/1.7-GCC-4.9.3, Canu/1.8-GCC-6.2.0 Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing (such as the PacBio RSII or Oxford Nanopore MinION). CapnProto: CapnProto/0.6.1-GCC-6.2.0 Cap’n Proto is an insanely fast data interchange format and capability-based RPC system. Charm++: Charm++/6.6.1-intel-2016.u3 Charm++ is a message-passing parallel language and runtime system. It is implemented as a set of libraries for C++, is efficient, and is portable to a wide variety of parallel machines. Source code is provided, and non-commercial use is free. Chaste: Chaste/2017.1-intel-2016.u3 Chaste (Cancer, Heart and Soft Tissue Environment) is a general purpose simulation package aimed at multi-scale, computationally demanding problems arising in biology and physiology. Current functionality includes tissue and cell level electrophysiology, discrete tissue modelling, and soft tissue modelling. CheMPS2: CheMPS2/1.6-intel-2016.u3 Circos: Circos/0.69-3-intel-2016.u3-Perl-5.20.0 CisTEM: CisTEM/1.0.0-beta-intel-linux cisTEM is user-friendly software to process cryo-EM images and obtain high-resolution 3D reconstructions from them. Its name derives from âmputational imaging system for transmission electron microscopyâses a number of tools to process image data including movies, micrographs and stacks of single-particle images. ClonalFrameML: ClonalFrameML/20160309-intel-2016.u3 ClonalFrameML is a software package that performs efficient inference of recombination in bacterial genomes. ClonalFrameML was created by Xavier Didelot and Daniel Wilson. ClonalFrameML can be applied to any type of aligned sequence data, but is especially aimed at analysis of whole genome sequences. It is able to compare hundreds of whole genomes in a matter of hours on a standard Desktop computer. Cloudy: Cloudy/17.01-GCC-4.9.2 Cloudy is a spectral synthesis code designed to simulate conditions in interstellar matter under a broad range of conditions. Code_Saturne: Code_Saturne/4.0.0-intel-2016.u3 Code_Saturne solves the Navier-Stokes equations for 2D, 2D-axisymmetric and 3D flows - Homepage: http://code-saturne.org Coinhsl: Coinhsl/2014.01.10-goolf-2015a HSL provides a number of linear solvers that can be used in IPOPT. - Homepage: http://www.hsl.rl.ac.uk/ipopt/ ConnectomeWorkbench: ConnectomeWorkbench/1.3.2-intel-2017.u2 CppUnit: CppUnit/r606-GCC-4.9.2, CppUnit/1.12.1-intel-2016.u3 CppUnit is the C++ port of the famous JUnit framework for unit testing. - Homepage: http://sourceforge.net/projects/cppunit/ Cube: Cube/4.2-goolf-2015a, Cube/4.3.4-goolf-2015a Cube, which is used as performance report explorer for Scalasca and Score-P, is a generic tool for displaying a multi-dimensional performance space consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree can be collapsed or expanded to achieve the desired level of granularity. Cufflinks: Cufflinks/2.2.1-GCC-4.9.2, Cufflinks/2.2.1-intel-2016.u3 Cython: Cython/0.28.5-intel-2017.u2-Python-2.7.11 The Cython language makes writing C extensions for the Python language as easy as Python itself. Cython is a source code translator based on the well-known Pyrex, but supports more cutting edge functionality and optimizations. DALTON: DALTON/2016-spartan_intel-2017.u2, ... Dalton program is designed to allow convenient, automated determination of a large number of molecular properties based on an HF, DFT, MP2, coupled cluster, or MCSCF reference wave function. DB: DB/2.7.7-GCC-4.9.2, DB/2.7.7-intel-2016.u3, DB/2.7.7-intel-2018.u4, ... DB_File: DB_File/1.831-intel-2016.u3-Perl-5.20.0-bare, ... Perl5 access to Berkeley DB version 1.x. DBus: DBus/1.10.12-goolf-2015a, DBus/1.10.12-intel-2016.u3, ... D-Bus is a message bus system, a simple way for applications to talk to one another. In addition to interprocess communication, D-Bus helps coordinate process lifecycle; it makes it simple and reliable to code a "single instance" application or daemon, and to launch applications and daemons on demand when their services are needed. DSRC: DSRC/2.0rc-linux-64-bit DNA Sequence Reads Compression is an application designed for compression of data files containing reads from DNA sequencing in FASTQ format. The amount of such files can be huge, e.g., a few (or tens) of gigabytes, so a need for a robust data compression tool is clear. Usually universal compression programs like gzip or bzip2 are used for this purpose, but it is obvious that a specialized tool can work better. Delft3D: Delft3D/3.80.00-intel-2016.u3, Delft3D/7545-intel-2016.u3 Delft3D is a world leading 3D modeling suite to investigate hydrodynamics, sediment transport and morphology and water quality for fluvial, estuarine and coastal environments. DendroPy: DendroPy/4.1.0-intel-2016.u3-Python-2.7.10, ... DendroPy is a Python library for phylogenetic computing. It provides classes and functions for the simulation, processing, and manipulation of phylogenetic trees and character matrices, and supports the reading and writing of phylogenetic data in a range of formats, such as NEXUS, NEWICK, NeXML, Phylip, FASTA, etc. Doxygen: Doxygen/1.8.8-GCC-4.9.2, Doxygen/1.8.8-intel-2016.u3, ... Doxygen is a documentation system for C++, C, Java, Objective-C, Python, IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D. - Homepage: http://www.doxygen.org EMAN2: EMAN2/2.12-intel-2016.u3-Python-2.7.9, ... EMAN2 is the successor to EMAN1. It is a broadly based greyscale scientific image processing suite with a primary focus on processing data from transmission electron microscopes. EMBOSS: EMBOSS/6.6.0-intel-2016.u3, EMBOSS/6.6.0-spartan_intel-2017.u2 EasyBuild: EasyBuild/2.4.0, EasyBuild/2.5.0, EasyBuild/2.9.0, ... EasyDict: EasyDict/1.8-intel-2016.u3-Python-3.5.2 EasyDict allows to access dict values as attributes (works recursively). A Javascript-like properties dot notation for python dicts.. Eigen: Eigen/3.2.3-GCC-4.9.2, Eigen/3.2.3-intel-2016.u3, ... Emacs: Emacs/25.3-GCC-4.9.2, Emacs/25.3-GCC-4.9.3 Emacs runs on several operating systems regardless of the machine type. The main ones are: GNU, GNU/Linux, FreeBSD, NetBSD, OpenBSD, macOS, MS Windows and Solaris. Env-Path: Env-Path/0.19-intel-2016.u3-Perl-5.20.0 Advanced operations on path variables Exonerate: Exonerate/2.2.0-intel-2016.u3 Exonerate is a generic tool for pairwise sequence comparison. It allows you to align sequences using a many alignment models, using either exhaustive dynamic programming, or a variety of heuristics. FASTX-Toolkit: FASTX-Toolkit/0.0.14-GCC-4.9.2 FDS: FDS/6.5.2-intel-2016.u3, FDS/6.7.0-spartan_intel-2017.u2 Fire Dynamics Simulator (FDS) is a large-eddy simulation (LES) code for low-speed flows, with an emphasis on smoke and heat transport from fires. - Homepage: https://pages.nist.gov/fds-smv/ FFC: FFC/1.6.0-intel-2016.u3-Python-2.7.9, ... FEniCS Form Compiler (FFC) works as a compiler for multilinear forms by generating code (C++) for the evaluation of a multilinear form given in mathematical notation. - Homepage: https://bitbucket.org/fenics-project/ffc FFTW: FFTW/2.1.5-intel-2016.u3, FFTW/3.3.4-GCC-4.9.2, ... FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data. - Homepage: http://www.fftw.org FFmpeg: FFmpeg/3.1.3-GCC-4.9.2, FFmpeg/3.1.3-intel-2016.u3, ... A complete, cross-platform solution to record, convert and stream audio and video. FIAT: FIAT/1.5.0-goolf-2015a-Python-2.7.10, ... The FInite element Automatic Tabulator FIAT supports generation of arbitrary order instances of the Lagrange elements on lines, triangles, and tetrahedra. It is also capable of generating arbitrary order instances of Jacobi-type quadrature rules on the same element shapes. FLASH: FLASH/1.2.11 FLASH (Fast Length Adjustment of SHort reads) is a very fast and accurate software tool to merge paired-end reads from next-generation sequencing experiments. FLASH is designed to merge pairs of reads when the original DNA fragments are shorter than twice the length of reads. FLTK: FLTK/1.3.3-intel-2016.u3, FLTK/1.3.3-intel-2017.u2 FLTK is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), Microsoft Windows, and MacOS X. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGL and its built-in GLUT emulation. - Homepage: http://www.fltk.org FSL: FSL/5.0.8-intel-2016.u3, FSL/5.0.9-centos6_64, ... FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data. FTGL: FTGL/2.1.3-rc5-intel-2016.u3 FTGL is a free open source library to enable developers to use arbitrary fonts in their OpenGL (www.opengl.org) applications. FastEpistasis: FastEpistasis/2.07-intel-2016.u3 FastEpistasis, a software tool capable of computing tests of epistasis for a large number of SNP pairs, is an efficient parallel extension to the PLINK epistasis module. FastTree: FastTree/2.1.7-intel-2016.u3, FastTree/2.1.8-intel-2016.u3, ... FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of time and memory. File-Grep: File-Grep/0.02-intel-2016.u3-Perl-5.20.0 Find matches to a pattern in a series of files and related functions File-Slurper: File-Slurper/0.008-intel-2016.u3-Perl-5.20.0 A simple, sane and efficient module to slurp a file FileShareDir: FileShareDir/1.102-intel-2016.u3-Perl-5.20.0 The intent of File::ShareDir is to provide a companion to Class::Inspector and File::HomeDir, modules that take a process that is well-known by advanced Perl developers but gets a little tricky, and make it more available to the larger Perl community. Filtlong: Filtlong/0.2.0-spartan_gcc-6.2.0 Filtlong is a tool for filtering long reads by quality.. Flye: Flye/2.4-intel-2017.u2-Python-2.7.13 Flye is a de novo assembler for long and noisy reads, such as those produced by PacBio and Oxford Nanopore Technologies. Fox: Fox/1.6.54-GCC-4.9.2 "FOX stands for Free Objects for X. It is a C++ based class library for building Graphical User Interfaces. - Homepage: http://www.fox-toolkit.org/ FragGeneScan: FragGeneScan/1.3.0-intel-2016.u3, ... FragGeneScan is an application for finding (fragmented) genes in short reads. It can also be applied to predict prokaryotic genes in incomplete assemblies or complete genomes. FreeSurfer: FreeSurfer/5.3.0-GCC-4.9.2-centos6_x86_64, ... FriBidi: FriBidi/1.0.1-intel-2018.u4 FriBidi is a free implementation of the Unicode Bidirectional (BiDi) Algorithm. It also provides utility functions to aid in the development of interactive editors and widgets that implement BiDi functionality. The BiDi algorithm is a prerequisite for supporting right-to-left scripts such as Hebrew, Arabic, Syriac, and Thaana. GAMESS-US: GAMESS-US/20160708-GCC-4.9.2 GAMS: GAMS/24.1 GATK: GATK/3.3-0-Java-1.7.0_80, GATK/3.4-46-Java-1.8.0_71, ... The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size. GCC: GCC/4.4.7, GCC/4.6.4, GCC/4.7.4, GCC/4.8.1, GCC/4.9.2-binutils-2.25, ... GCC-CUDA: GCC-CUDA/5.4.0-8.0.61, GCC-CUDA/6.2.0-9.0.176 The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...). This version also GCCcore: GCCcore/5.4.0, GCCcore/6.3.0, GCCcore/6.4.0, GCCcore/7.3.0, ... The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...). GConf: GConf/3.2.6-GCC-6.2.0, GConf/3.2.6-intel-2017.u2 GConf is a system for storing application preferences. It is intended for user preferences; not configuration of something like Apache, or arbitrary data storage. GD: GD/2.52-intel-2016.u3-Perl-5.20.0, GD/2.56-intel-2016.u3-Perl-5.20.0 GDAL: GDAL/1.10.0-GCC-4.9.2, GDAL/1.10.0-intel-2016.u3, ... GDB: GDB/7.8.2-GCC-4.9.2, GDB/7.8.2-goolf-2015a GEMINI: GEMINI/0.18.3-GCC-4.9.2-Python-2.7.9 GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics. GEOS: GEOS/3.6.1-intel-2016.u3-Python-2.7.11, ... GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS) GHC: GHC/6.12.3-GCC-4.9.2, GHC/6.12.3-intel-2016.u3 The Glorious/Glasgow Haskell Compiler GLINT: GLINT/1.0.4-Python.2.7.13-intel-2017.u2 GLINT is a user-friendly command-line tool for fast analysis of genome-wide DNA methylation data generated using the Illumina human methylation arrays. GLINT allows to easily run a pipeline of Epigenome-Wide Association Study (EWAS) under different models while accounting for known confounders in methylation data. GLM: GLM/0.9.7.2-intel-2016.u3, GLM/0.9.7.2-intel-2017.u2 OpenGL Mathematics (GLM) is a header only C++ mathematics library for graphics software based on the OpenGL Shading Language (GLSL) specifications. - Homepage: https://github.com/g-truc/glm GLib: GLib/2.40.0-intel-2016.u3, GLib/2.46.0-intel-2016.u3-Python-2.7.9, ... GMAP-GSNAP: GMAP-GSNAP/2014-06-10-GCC-4.9.2 GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences GSNAP: Genomic Short-read Nucleotide Alignment Program GMP: GMP/5.1.3-GCC-4.9.2, GMP/6.0.0a-GCC-4.9.2, GMP/6.0.0a-GCC-4.9.3, ... GMSH: GMSH/2.16.0-intel-2016.u3 Gmsh is a 3D finite element grid generator with a build-in CAD engine and post-processor. - Homepage: http://geuz.org/gmsh GNU: GNU/4.9.2-2.25 Compiler-only toolchain with GCC and binutils. - Homepage: http://www.gnu.org/software/ GObject-Introspection: GObject-Introspection/1.47.1-GCC-4.9.2, ... GObject introspection is a middleware layer between C libraries (using GObject) and language bindings. The C library can be scanned at compile time and generate a metadata file, in addition to the actual native C library. Then at runtime, language bindings can read this metadata and automatically provide bindings to call into the C library. - Homepage: https://wiki.gnome.org/GObjectIntrospection/ GROMACS: GROMACS/4.6.5-intel-2016.u3-mpi, GROMACS/4.6.5-intel-2016.u3-mt, ... GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. GSL: GSL/1.16-intel-2016.u3, GSL/1.16-spartan_intel-2017.u2, ... GST-plugins-base: GST-plugins-base/0.10.36-GCC-6.2.0, ... GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio (mixing) and video (non-linear editing) processing. GStreamer: GStreamer/0.10.36-GCC-6.2.0, GStreamer/0.10.36-intel-2017.u2, ... GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio (mixing) and video (non-linear editing) processing. GTK+: GTK+/2.24.28-intel-2016.u3, GTK+/2.24.31-GCC-4.9.2, ... The GTK+ 2 package contains libraries used for creating graphical user interfaces for applications. - Homepage: https://developer.gnome.org/gtk+/stable/ GTS: GTS/0.7.6-intel-2018.u4 GTS stands for the GNU Triangulated Surface Library. It is an Open Source Free Software Library intended to provide a set of useful functions to deal with 3D surfaces meshed with interconnected triangles. Gaussian: Gaussian/g09.b01, Gaussian/g09TEST, Gaussian/g09, Gaussian/g16 Gdk-Pixbuf: Gdk-Pixbuf/2.32.3-intel-2016.u3, Gdk-Pixbuf/2.36.6-GCC-4.9.2, ... The Gdk Pixbuf is a toolkit for image loading and pixel buffer manipulation. It is used by GTK+ 2 and GTK+ 3 to load and manipulate images. In the past it was distributed as part of GTK+ 2 but it was split off into a separate package in preparation for the change to GTK+ 3. - Homepage: https://developer.gnome.org/gdk-pixbuf/stable/ Gensim: Gensim/3.7.1-intel-2016.u3-Python-2.7.12, ... Scalable statistical semantics, Analyze plain-text documents for semantic structure, Retrieve semantically similar documents Ghostscript: Ghostscript/9.20-intel-2016.u3, ... Ghostscript is a versatile processor for PostScript data with the ability to render PostScript to different targets. It used to be part of the cups printing stack, but is no longer used for that. Go: Go/1.5.1, Go/1.8.1, Go/1.11.5 Go is an open source programming language that makes it easy to build simple, reliable, and efficient software. GrADS: GrADS/2.2.0-GCC-4.9.2 The Grid Analysis and Display System (GrADS) is an interactive desktop tool that is used for easy access, manipulation, and visualization of earth science data. Graph: Graph/0.9704-intel-2016.u3-Perl-5.20.0 graph data structures and algorithms Graphviz: Graphviz/2.40.1-intel-2018.u4 Graphviz is open source graph visualization software. Graph visualization is a way of representing structural information as diagrams of abstract graphs and networks. It has important applications in networking, bioinformatics, software engineering, database and web design, machine learning, and in visual interfaces for other technical domains. Greenlet: Greenlet/0.4.9-intel-2016.u3-Python-3.5.2 The greenlet package is a spin-off of Stackless, a version of CPython that supports micro-threads called "tasklets". Tasklets run pseudo-concurrently (typically in a single or a few OS-level threads) and are synchronized with data exchanges on "channels". A "greenlet", on the other hand, is a still more primitive notion of micro-thread with no implicit scheduling; coroutines, in other words. This is useful when you want to control exactly when your code runs. Gubbins: Gubbins/1.4.2-intel-2016.u3-Python-2.7.9, ... Gubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences) is an algorithm that iteratively identifies loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the putative point mutations outside of these regions. - Homepage: https://github.com/andrewjpage/gubbins Guppy: Guppy/2.3.1-cpu, Guppy/2.3.1-rpm Guppy software supports MinIT and MinION instruments from Nanopore Technologies Gurobi: Gurobi/7.0.1 The Gurobi Optimizer is a state-of-the-art solver for mathematical programming. The solvers in the Gurobi Optimizer were designed from the ground up to exploit modern architectures and multi-core processors, using the most advanced implementations of the latest algorithms. - Homepage: http://www.gurobi.com HDF: HDF/4.2.8-GCC-4.9.2, HDF/4.2.8-intel-2016.u3 HDF5: HDF5/1.8.12-intel-2016.u3, HDF5/1.8.13-GCC-4.9.2, ... HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections. - Homepage: http://www.hdfgroup.org/HDF5/ HGA: HGA/1.0.0-Python-2.7.10 Hierarchical Genome Assembly (HGA) is a novel methodology that takes further advantage of very high coverage by independently assembling disjoint subsets of reads, combining assemblies of the subsets, and finally re-assembling the combined contigs along with the original reads. HGA_pymodules-bundle: ... This is a bundle of two python modules, xlrd and xlwt, required by the application, HGA (separate module). xlrd (https://pypi.python .org/pypi/xlrd) extracts data from Microsoft Excel spreadsheets, while xlwt (https://pypi.python.org/pypi/xlwt) is used to generate Excel spreadsheet s. HISAT2: HISAT2/2.1.0-intel-2016.u3 HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome). - Homepage: https://ccb.jhu.edu/software/hisat2/index.shtml HMMER: HMMER/3.1b2-intel-2016.u3, HMMER/3.1b2-intel-2017.u2 HPL: HPL/2.1-intel-2016.u3 HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the High Performance Computing Linpack Benchmark. HTSeq: HTSeq/0.9.1-intel-2016.u3-Python-2.7.12 - Homepage: http://www-huber.embl.de/users/anders/HTSeq/ HTSlib: HTSlib/1.2.1-intel-2016.u3, HTSlib/1.3-intel-2016.u3, ... A C library for reading/writing high-throughput sequencing data. This package includes the utilities bgzip and tabix HarfBuzz: HarfBuzz/1.1.3-GCC-4.9.2, HarfBuzz/1.1.3-goolf-2015a, ... HarfBuzz is an OpenType text shaping engine. - Homepage: http://www.freedesktop.org/wiki/Software/HarfBuzz Hypre: Hypre/2.11.1-goolf-2015a, Hypre/2.11.1-intel-2016.u3-test, ... Hypre is a library for solving large, sparse linear systems of equations on massively parallel computers. The problems of interest arise in the simulation codes being developed at LLNL and elsewhere to study physical phenomena in the defense, environmental, energy, and biological sciences. I-TASSER: I-TASSER/4.2, I-TASSER/5.0 I-TASSER (Iterative Threading ASSEmbly Refinement) is a hierarchical method for protein structure and function prediction. Structural templates are identified from the PDB by multiple threading approach LOMETS; full-length atomic models are then constructed by iterative template fragment assembly simulations; function inslights of the target are finally derived by threading the 3D models through protein function database BioLiP. ICU: ICU/60.2-GCC-4.9.2, ICU/61.1-intel-2017.u2, ICU/61.1-intel-2018.u4 ICU is a mature, widely used set of C/C++ and Java libraries providing Unicode and Globalization support for software applications. ICU is widely portable and gives applications the same results on all platforms and between C/C++ and Java software. . IDBA: IDBA/1.1.3-GCC-4.9.3, IDBA/1.1.3-intel-2017.u2 IDBA is the basic iterative de Bruijn graph assembler for second-generation sequencing reads. IDBA-UD, an extension of IDBA, is designed to utilize paired-end reads to assemble low-depth regions and use progressive depth on contigs to reduce errors in high-depth regions. IGV: IGV/2.3.15 The Integrative Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large, integrated genomic datasets. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations. IOR: IOR/3.0.1-gompi-2015a-mpiio The IOR software is used for benchmarking parallel file systems using POSIX, MPIIO, or HDF5 interfaces. - Homepage: https://github.com/chaos/ior IPC-System-Simple: IPC-System-Simple/1.25-intel-2016.u3-Perl-5.20.0 IPC::System::Simple - Run commands simply, with detailed diagnostics. IPython: IPython/3.2.0-intel-2016.u3-Python-2.7.9 IPython provides a rich architecture for interactive computing with: Powerful interactive shells (terminal and Qt-based). A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. Support for interactive data visualization and use of GUI toolkits. Flexible, embeddable interpreters to load into your own projects. Easy to use, high performance tools for parallel computing. - Homepage: http://ipython.org/index.html ISL: ISL/0.15-GCC-4.9.2 ITK: ITK/4.12.2-intel-2016.u3-Python-2.7.11 Insight Segmentation and Registration Toolkit (ITK) provides an extensive suite of software tools for registering and segmenting multidimensional imaging data. ImageMagick: ImageMagick/7.0.2-9-GCC-4.9.2, ImageMagick/7.0.2-9-GCC-6.2.0 Infernal: Infernal/1.1.2-intel-2016.u3 Instant: Instant/1.6.0-intel-2016.u3-Python-2.7.9, ... Instant is a Python module that allows for instant inlining of C and C++ code in Python. It is a small Python module built on top of SWIG and Distutils. - Homepage: https://bitbucket.org/fenics-project/instant InterViews: InterViews/19-intel-2016.u3, InterViews/19-intel-2017.u2 InterViews is a prerequisite of the NEURON, a simulation environment for building and using computational models of neurons and networks of neurons. JAGS: JAGS/4.2.0-intel-2016.u3, JAGS/4.3.0-GCC-6.2.0, ... JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation - Homepage: http://mcmc-jags.sourceforge.net/ JUnit: JUnit/4.12-Java-1.8.0_71, JUnit/4.12-Java-9.0.4 A programmer-oriented testing framework for Java. - Homepage: http://sourceforge.net/projects/junit JasPer: JasPer/1.900.1-GCC-4.9.2, JasPer/1.900.1-intel-2016.u3, ... Java: Java/1.7.0_80, Java/1.8.0_71, Java/1.8.0_152, Java/9.0.4 Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers. Jellyfish: Jellyfish/1.1.11-GCC-4.9.2, Jellyfish/2.2.6-spartan_gcc-6.2.0, ... Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. Json-Fortran: Json-Fortran/6.3.0-GCC-6.2.0, ... A user-friendly, thread-safe, and object-oriented API for reading and writing JSON files, written in modern Fortran. Julia: Julia/0.5.0-binary, Julia/0.6.0-binary, ... KNIFE: KNIFE/1.4 Known and Novel IsoForm Explorer. Statistically based splicing detection for circular and linear isoforms from RNA-Seq data. Kaiju: Kaiju/1.6.2-intel-2017.u2 Kaiju is a program for sensitive taxonomic classification of high-throughput sequencing reads from metagenomic whole genome sequencing experiments Kent_tools: Kent_tools/20181018-linux.x86_64 Kent tools: collection of tools used by the UCSC genome browser. Keras: Keras/2.1.5-intel-2017.u2-GCC-5.4.0-CUDA8-Python-3.5.2-GPU, ... Keras is a high-level neural networks API, written in Python and capable of running on top of TensorFlow, CNTK, or Theano. Kraken: Kraken/1.0-GCC-4.9.2, Kraken/1.0-intel-2017.u2-Perl-5.24.1, ... Kraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Kraken2: Kraken2/2.0.6-beta-intel-2016.u3-Perl-5.26.2 Kraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. Kraken aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm. Krona: Krona/2.7 Krona allows hierarchical data to be explored with zooming, multi-layered pie charts. KyotoCabinet: KyotoCabinet/1.2.76-intel-2016.u3 Kyoto Cabinet is a library of routines for managing a database. LAMMPS: LAMMPS/20170811-goolfc-2017.01, ... LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) is a classical molecular dynamics simulation code designed to run efficiently on parallel computers. LAPACK: LAPACK/3.4.2-GCC-6.2.0, ... LAPACK is written in Fortran90 and provides routines for solving systems of simultaneous linear equations, least-squares solutions of linear systems of equations, eigenvalue problems, and singular value problems. LLVM: LLVM/3.7.0-GCC-4.9.2, LLVM/3.7.0-goolf-2015a, ... The LLVM Core libraries provide a modern source- and target-independent optimizer, along with code generation support for many popular CPUs (as well as some less common ones!) These libraries are built around a well specified code representation known as the LLVM intermediate representation ("LLVM IR"). The LLVM Core libraries are well documented, and it is particularly easy to invent your own language (or port an existing compiler) to use LLVM as an optimizer and code generator. - Homepage: http://llvm.org/ LMDB: LMDB/0.9.18-GCC-4.9.2, LMDB/0.9.18-intel-2016.u3, ... OpenLDAP's Lightning Memory-Mapped Database (LMDB) library. - Homepage: https://github.com/LMDB/lmdb LZO: LZO/2.10-intel-2017.u2 Portable lossless data compression library LibTIFF: LibTIFF/4.0.4-goolf-2015a, LibTIFF/4.0.4-intel-2016.u3, ... tiff: Library and tools for reading and writing TIFF data files - Homepage: http://www.remotesensing.org/libtiff/ LibUUID: LibUUID/1.0.3-intel-2016.u3, LibUUID/1.0.3-intel-2017.u2 Portable uuid C library LightGBM: LightGBM/2.1.0-GCC-4.9.2 A fast, distributed, high performance gradient boosting (GBDT, GBRT, GBM or MART) framework based on decision tree algorithms. LittleCMS: LittleCMS/2.7-goolf-2015a, ... Little CMS intends to be an OPEN SOURCE small-footprint color management engine, with special focus on accuracy and performance. Lua: Lua/5.1.4-8-GCC-4.9.2, Lua/5.1.4-8-intel-2016.u3, ... Lua is a powerful, fast, lightweight, embeddable scripting language. Lua combines simple procedural syntax with powerful data description constructs based on associative arrays and extensible semantics. Lua is dynamically typed, runs by interpreting bytecode for a register-based virtual machine, and has automatic memory management with incremental garbage collection, making it ideal for configuration, scripting, and rapid prototyping. - Homepage: http://www.lua.org/ M4: M4/1.4.17-foss-2017b, M4/1.4.17-GCC-4.6.4, ... MAFFT: MAFFT/7.130-GCC-4.9.2-with-extensions, ... MATIO: MATIO/1.5.2-intel-2016.u3, MATIO/1.5.2-intel-2017.u2 matio is an C library for reading and writing Matlab MAT files. - Homepage: http://sourceforge.net/projects/matio/ MATLAB: MATLAB/2016a, MATLAB/2017a, MATLAB/2018a, MATLAB/2018b MATLAB is a high-level language and interactive environment that enables you to perform computationally intensive tasks faster than with traditional programming languages such as C, C++, and Fortran. MCL: MCL/14.137-intel-2016.u3, MCL/14.137-spartan_gcc-6.2.0, ... MCR: MCR/R2016a The MATLAB Runtime is a standalone set of shared libraries that enables the execution of compiled MATLAB applications or components on computers that do not have MATLAB installed. MEGA: MEGA/10.0.5 MEGA-CC (Molecular Evolutionary Genetics Analysis Computational Core) is an integrated suite of tools for statistics-based comparative analysis of molecular sequence data based on evolutionary principles. MEGAHIT: MEGAHIT/1.0.3-intel-2016.u3, MEGAHIT/1.1.1-intel-2016.u3, ... MEGAHIT is a NGS de novo assembler for assembling large and complex metagenomics data in a time- and cost-efficient manner. METIS: METIS/3.0.6-intel-2017.u2, METIS/4.0.3-intel-2016.u3, ... METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the multilevel recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes. - Homepage: http://glaros.dtc.umn.edu/gkhome/metis/metis/overview MPC: MPC/1.0.2-GCC-4.9.2, MPC/1.0.2-intel-2016.u3 MPFR: MPFR/3.1.2-GCC-4.9.2, MPFR/3.1.2-intel-2016.u3, ... MPICH: MPICH/3.2.1-GCC-4.9.2, MPICH/3.2.1-GCC-6.2.0 MPICH v3.x is an open source high-performance MPI 3.0 implementation. It does not support InfiniBand (use MVAPICH2 with InfiniBand devices). MPJ-Express: MPJ-Express/0.44-goolf-2015a-Java-9.0.4 MPJ Express is an open source Java message passing library that allows application developers to write and execute parallel applications for multicore processors and compute clusters/clouds. MRtrix: MRtrix/0.3.14-intel-2016.u3-Python-2.7.9, ... MRtrix provides a set of tools to perform diffusion-weighted MR white-matter tractography in a manner robust to crossing fibres, using constrained spherical deconvolution (CSD) and probabilistic streamlines. - Homepage: http://www.brain.org.au/software/index.html#mrtrix MTL4: MTL4/4.0.9555 The Matrix Template Library 4 incorporates the most modern programming techniques to provide an easy and intuitive interface to users while enabling optimal performance. The natural mathematical notation in MTL4 empowers all engineers and scientists to implement their algorithms and models in minimal time. All technical aspects are encapsulated in the library. - Homepage: http://www.simunova.com/mtl4 MUMPS: MUMPS/4.10.0-goolf-2015a-parmetis, ... A parallel sparse direct solver - Homepage: http://graal.ens-lyon.fr/MUMPS/ MUMmer: MUMmer/3.23-intel-2016.u3 MUSCLE: MUSCLE/3.8.31-intel-2016.u3 Mako: Mako/1.0.4-GCC-6.2.0-Python-2.7.13-bare, ... A super-fast templating language that borrows the best ideas from the existing templating languages Maple: Maple/2015 MariaDB-connector-c: MariaDB-connector-c/2.3.5-GCC-6.2.0, ... MariaDB Connector/C is used to connect applications developed in C/C++ to MariaDB and MySQL databases. Mash: Mash/2.1-intel-2017.u2 Fast genome and metagenome distance estimation using MinHash Mathematica: Mathematica/11.0.1 Mathematica is a computational software program used in many scientific, engineering, mathematical and computing fields. - Homepage: http://www.wolfram.com/mathematica Maven: Maven/3.5.4 Binary maven install, Apache Maven is a software project management and comprehension tool. Based on the concept of a project object model (POM), Maven can manage a project's build, reporting and documentation from a central piece of information. MaxBin: MaxBin/2.2.5-intel-2017.u2 MaxBin is a software that is capable of clustering metagenomic contigs into different bins, each consists of contigs from one species. MaxBin uses the nucleotide composition information and contig abundance information to do achieve binning through an Expectation-Maximization algorithm. Maxima: Maxima/5.41.0-GCC-6.2.0, Maxima/5.41.0-GCCcore-6.4.0 Maxima is a system for the manipulation of symbolic and numerical expressions. Mesa: Mesa/7.11.2-GCC-4.9.2-Python-2.7.9, ... Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics. - Homepage: http://www.mesa3d.org/ Meson: Meson/0.43.0-intel-2016.u3-Python-3.5.2, ... Meson is a cross-platform build system designed to be both as fast and as user friendly as possible. MetaBAT: MetaBAT/2.12.1-intel-2017.u2 Benchmark of Automated Metagenome Binning Software in Complex Metagenomes. MetaVelvet: MetaVelvet/1.2.01-intel-2016.u3, ... Miniasm: Miniasm/0.3-GCC-6.2.0 Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. Miniconda2: Miniconda2/4.3.21 Built to complement the rich, open source Python community, the Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture. Miniconda3: Miniconda3/4.4.10, Miniconda3/4.5.4 Built to complement the rich, open source Python community, the Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture. Minimac3: Minimac3/1.0.10-intel-2016.u3, Minimac3/2.0.1-intel-2016.u3 Minimac3 is a lower memory and more computationally efficient implementation of the genotype imputation algorithms in minimac and minimac2. Minimac3 is designed to handle very large reference panels in a more computationally efficient way with no loss of accuracy. - Homepage: http://genome.sph.umich.edu/wiki/Minimac3 Minimap2: Minimap2/2.13-intel-2017.u2, Minimap2/2.15-GCC-6.2.0 Minimap2 is a versatile sequence alignment program that aligns DNA or mRNA sequences against a large reference database. Molden: Molden/5.7-GCC-4.9.2, Molden/5.7-intel-2016.u3 Molden is a package for displaying Molecular Density from the Ab Initio packages GAMESS-UK, GAMESS-US and GAUSSIAN and the Semi-Empirical packages Mopac/Ampac - Homepage: http://www.cmbi.ru.nl/molden/ Mono: Mono/4.6.2.7-GCC-4.9.2, Mono/4.6.2.7-intel-2016.u3, ... An open source, cross-platform, implementation of C# and the CLR that is binary compatible with Microsoft.NET. - Homepage: http://mono-framework.com MotionCor2: MotionCor2/01-30-2017 Correction of electron beam-induced sample motion is one of the major factors contributing to the recent resolution breakthroughs in cryo-electron microscopy. - Homepage: http://msg.ucsf.edu/em/software/motioncor2.html MrBayes: MrBayes/3.2.6-intel-2016.u3 MrBayes is a program for the Bayesian estimation of phylogeny. MultiQC: MultiQC/1.6-intel-2017.u2-Python-3.6.4 Aggregate results from bioinformatics analyses across many samples into a single report. MultiQC searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. Multiwell: Multiwell/2016-intel-2016.u3 Calculates time dependent concentrations, reaction yields, vibrational distributions, and rate constants as functions of temperature and pressure for multi-well, multi-channel unimolecular reactions systems. - Homepage: http://clasp-research.engin.umich.edu/multiwell/ NAMD: NAMD/2.10-gompi-2015a-mpi, NAMD/2.10-intel-2016.u3-mpi, ... NASM: NASM/2.11.06-intel-2016.u3, NASM/2.11.08-foss-2017b, ... NASM: General-purpose x86 assembler NCBI-GENOME: NCBI-GENOME/0.2.2-intel-2016.u3-Python-2.7.10 Some script to download bacterial and fungal genomes from NCBI after they restructured their FTP a while ago. NCBI-Toolkit: NCBI-Toolkit/21.0.0-intel-2017.u2 The NCBI Toolkit is a collection of utilities developed for the production and distribution of GenBank, Entrez, BLAST, and related services by the National Center for Biotechnology Information. NCL: NCL/6.5.0 NCAR Command Language NCO: NCO/4.7.1-intel-2016.u3, NCO/4.7.1-intel-2017.u2 manipulates and analyzes data stored in netCDF-accessible formats, including DAP, HDF4, and HDF5 NEURON: NEURON/7.4-gompi-2015a, NEURON/7.4-intel-2016.u3, ... Empirically-based simulations of neurons and networks of neurons. - Homepage: http://www.neuron.yale.edu/neuron NEdit: NEdit/5.5-Linux-x86 NEdit is a multi-purpose text editor for the X Window System, which combines a standard, easy to use, graphical user interface with the thorough functionality and stability required by users who edit text eight hours a day. NGS: NGS/2.9.3-spartan_intel-2017.u2-Java-1.8.0_152 NGS is a new, domain-specific API for accessing reads, alignments and pileups produced from Next Generation Sequencing. NLopt: NLopt/2.4.2-intel-2017.u2, NLopt/2.4.2-intel-2018.u4, ... NLopt is a free/open-source library for nonlinear optimization, providing a common interface for a number of different free optimization routines available online as well as original implementations of various other algorithms. NSPR: NSPR/4.9.3-GCC-6.2.0 Netscape Portable Runtime (NSPR) provides a platform-neutral API for system level and libc-like functions. The API is used in the Mozilla clients, many of Red Hat's and Oracle's server applications, and other software offerings. NWChem: NWChem/6.5.revision26243-intel-2016.u3-2014-09-10-Python-2.7.11 NWChem aims to provide its users with computational chemistry tools that are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters. NWChem software can handle: biomolecules, nanostructures, and solid-state; from quantum to classical, and all combinations; Gaussian basis functions or plane-waves; scaling from one to thousands of processors; properties and relativity. - Homepage: http://www.nwchem-sw.org NanoOK: NanoOK/1.33-intel-2017.u2-Java-9 NanoOK (pronounced na-nook) is a tool for extraction, alignment and analysis of Nanopore reads. NanoOK will extract reads as FASTA or FASTQ files, align them (with a choice of alignment tools), then generate a comprehensive multi-page PDF report containing yield, accuracy and quality analysis. NiBabel: NiBabel/2.1.0-intel-2016.u3-Python-2.7.9-freetype-2.6.5 NiBabel provides read/write access to some common medical and neuroimaging file formats, including: ANALYZE (plain, SPM99, SPM2 and later), GIFTI, NIfTI1, NIfTI2, MINC1, MINC2, MGH and ECAT as well as Philips PAR/REC. We can read and write Freesurfer geometry, and read Freesurfer morphometry and annotation files. There is some very limited support for DICOM. NiBabel is the successor of PyNIfTI. - Homepage: https://nipy.github.io/nibabel Nilearn: Nilearn/0.1.3-intel-2016.u3-Python-2.7.9-freetype-2.6.5 Nilearn is a Python module for fast and easy statistical learning on NeuroImaging data. - Homepage: http://nilearn.github.io/ Ninja: Ninja/1.8.2-intel-2016.u3, Ninja/1.8.2-intel-2017.u2, ... Ninja is a small build system with a focus on speed. OCaml: OCaml/4.01.0-intel-2017.u2 OCaml is a general purpose industrial-strength programming language with an emphasis on expressiveness and safety. Developed for more than 20 years at Inria it benefits from one of the most advanced type systems and supports functional, imperative and object-oriented styles of programming. OPARI2: OPARI2/1.1.1-goolf-2015a, OPARI2/1.1.2-goolf-2015a, ... OPARI2, the successor of Forschungszentrum Juelich's OPARI, is a source-to-source instrumentation tool for OpenMP and hybrid codes. It surrounds OpenMP directives and runtime library calls with calls to the POMP2 measurement interface. OPERA-MS: OPERA-MS/14Dec2018-spartan_gcc-6.2.0 OPERA-MS is a hybrid metagenomic assembler which combines the advantages of short and long-read technologies to provide high quality assemblies, addressing issues of low contiguity for short-read only assemblies, and low base-pair quality for long-read only assemblies. ORCA: ORCA/3_0_2-linux_x86-64-OpenMPI-1.6.5, ... OTF: OTF/1.12.4-goolf-2015a The Open Trace Format is a highly scalable, memory efficient event trace data format plus support library. It is the standard trace format for Vampir, and is open for other tools. [NOW OBSOLETE: use OTF2] OTF2: OTF2/1.2.1-goolf-2015a, OTF2/2.0-goolf-2015a The Open Trace Format 2 is a highly scalable, memory efficient event trace data format plus support library. It will become the new standard trace format for Scalasca, Vampir, and Tau and is open for other tools. Octave: Octave/3.8.2-goolf-2015a, Octave/4.2.1-goolf-2015a OlaFlow: OlaFlow/20170725-intel-2016.u3-OpenFOAM-4.0, ... This free and open source project is committed to bringing the latest advances in the simulation of wave dynamics to the OpenFOAM® and FOAM-extend communities. olaFlow includes a set of solvers and boundary conditions to generate and absorb water waves actively at the boundaries and to simulate their interaction with porous coastal structures. OpenBLAS: OpenBLAS/0.2.14-gompi-2015a-LAPACK-3.5.0, ... OpenBUGS: OpenBUGS/3.2.3 BUGS is a software package for performing Bayesian inference Using Gibbs Sampling. - Homepage: http://www.openbugs.net/ OpenCV: OpenCV/3.1.0-GCC-4.9.2, OpenCV/3.1.0-intel-2016.u3 OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library. OpenCV was built to provide a common infrastructure for computer vision applications and to accelerate the use of machine perception in the commercial products. OpenEXR: OpenEXR/2.2.0-intel-2016.u3 OpenEXR is a high dynamic-range (HDR) image file format developed by Industrial Light & Magic for use in computer imaging applications - Homepage: http://www.openexr.com/ OpenFOAM/1606+-intel-2016.u3: OpenFOAM/1606+-intel-2016.u3 OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics. - Homepage: http://www.openfoam.com/ OpenFOAM/2.1.1-gompi-GCC-4.6.4-OpenMPI-1.8.4: ... OpenFOAM/2.1.1-iompi-2016.u3: OpenFOAM/2.1.1-iompi-2016.u3 OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics. OpenFOAM/2.1.1-iompi-2016.u3-custom: OpenFOAM/2.1.1-iompi-2016.u3-custom OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics. OpenFOAM/2.3.1-intel-2016.u3: OpenFOAM/2.3.1-intel-2016.u3 OpenFOAM/2.3.1-iompi-2016.u3: OpenFOAM/2.3.1-iompi-2016.u3 OpenFOAM/2.4.0-intel-2016.u3: OpenFOAM/2.4.0-intel-2016.u3 OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics. OpenFOAM/2.4.0-intel-2017.u2: OpenFOAM/2.4.0-intel-2017.u2 OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics. OpenFOAM/4.0-intel-2016.u3: OpenFOAM/4.0-intel-2016.u3 OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics. - Homepage: http://www.openfoam.com/ OpenFOAM/5.0-intel-2017.u2: OpenFOAM/5.0-intel-2017.u2 OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics. OpenFOAM/5.0-intel-2017.u2-CUDA8-test: ... OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics. OpenFOAM/6-spartan_intel-2017.u2: OpenFOAM/6-spartan_intel-2017.u2 OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics. OpenFOAM/v1806-intel-2017.u2: OpenFOAM/v1806-intel-2017.u2 OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics. OpenImageIO: OpenImageIO/1.6.17-intel-2016.u3 OpenImageIO is a library for reading and writing images, and a bunch of related classes, utilities, and applications. - Homepage: http://openimageio.org/ OpenMM: OpenMM/7.2.1-intel-2017.u2-Python-3.6.1 OpenMM is a toolkit for molecular simulation. OpenMPI: OpenMPI/1.6.5-GCC-4.9.2, OpenMPI/1.8.4-GCC-4.6.4, ... The Open MPI Project is an open source MPI-2 implementation. OpenPGM: OpenPGM/5.2.122-intel-2016.u3 OpenPGM is an open source implementation of the Pragmatic General Multicast (PGM) specification in RFC 3208 available at www.ietf.org. PGM is a reliable and scalable multicast protocol that enables receivers to detect loss, request retransmission of lost data, or notify an application of unrecoverable loss. PGM is a receiver-reliable protocol, which means the receiver is responsible for ensuring all data is received, absolving the sender of reception responsibility. - Homepage: http://code.google.com/p/openpgm/ OpenSSL: OpenSSL/1.0.1p-GCC-4.9.2, OpenSSL/1.0.1p-GCC-4.9.3, ... OpenUCX: OpenUCX/1.3.0-CUDA9.1, OpenUCX/1.3.0, OpenUCX/1.4.x, ... UCX is a communication library implementing a high-performance messaging layer for MPI, PGAS, and RPC frameworks. OrfM: OrfM/0.7.1-goolf-2015a A simple and not slow open reading frame (ORF) caller. PAML: PAML/4.9a-intel-2016.u3 PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. PAPI: PAPI/5.2.0-gompi-2015a, PAPI/5.2.0-goolf-2015a, ... PAPI provides the tool designer and application engineer with a consistent interface and methodology for use of the performance counter hardware found in most major microprocessors. PAPI enables software engineers to see, in near real time, the relation between software performance and processor events. In addition Component PAPI provides access to a collection of components that expose performance measurement opportunites across the hardware and software stack. PARCAS: PARCAS/20181017-GCC-4.9.2 PCMSolver: PCMSolver/1.1.5-intel-2016.u3-Python-2.7.9 PCRE: PCRE/8.36-GCC-4.9.2, PCRE/8.36-GCC-6.2.0, PCRE/8.36-gompi-2015a, ... PDT: PDT/3.19-goolf-2015a, PDT/3.22-goolf-2015a, PDT/3.25-goolf-2015a Program Database Toolkit (PDT) is a framework for analyzing source code written in several programming languages and for making rich program knowledge accessible to developers of static and dynamic analysis tools. PDT implements a standard program representation, the program database (PDB), that can be accessed in a uniform way through a class library supporting common PDB operations. PEAR: PEAR/0.9.11-foss-2017b, PEAR/0.9.11-GCC-6.2.0, ... PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger. It is fully parallelized and can run with as low as just a few kilobytes of memory. PEST: PEST/15-GCC-6.2.0 Model-Independent Parameter Estimation and Uncertainty Analysis PEST-plproc: PEST-plproc/3.0-intel-2017.u2 PLPROC is a “parameter list processor”. It was written to expedite the use of PEST in conjunction with complex spatial models which may possess structured or unstructured grids. PETSc: PETSc/3.5.3-intel-2016.u3-Python-2.7.9, ... PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations. PGI: PGI/16.10-GCC-4.9.2-2.26, PGI/16.10-GCC-5.4.0-2.26, ... C, C++ and Fortran compilers from The Portland Group - PGI PIL: PIL/1.1.7-intel-2016.u3-Python-2.7.9-freetype-2.6.5, ... The Python Imaging Library (PIL) adds image processing capabilities to your Python interpreter. This library supports many file formats, and provides powerful image processing and graphics capabilities. - Homepage: http://www.pythonware.com/products/pil PLINK: PLINK/1.07-x86_64, PLINK/1.90-b5.3-x84-64, PLINK/1.90-b5.3-x86-64 plink-1.07-src: Whole-genome association analysis toolset PLY: PLY/3.8-intel-2016.u3-Python-2.7.9, ... PLY is yet another implementation of lex and yacc for Python. - Homepage: http://www.dabeaz.com/ply/ POI: POI/3.17-20170915-x86_64 The Apache POI Project's mission is to create and maintain Java APIs for manipulating various file formats based upon the Office Open XML standards (OOXML) and Microsoft's OLE 2 Compound Document format (OLE2). In short, you can read and write MS Excel files using Java. In addition, you can read and write MS Word and MS PowerPoint files using Java. Apache POI is your Java Excel solution (for Excel 97-2008). We have a complete API for porting other OOXML and OLE2 formats and welcome others to participate. PRANK: PRANK/140110-GCC-4.9.2, PRANK/140110-intel-2016.u3, ... PRANK is a probabilistic multiple alignment program for DNA, codon and amino-acid sequences. PRANK is based on a novel algorithm that treats insertions correctly and avoids over-estimation of the number of deletion events. PROJ: PROJ/4.8.0-intel-2016.u3, PROJ/4.9.2-GCC-4.9.2, ... Program proj is a standard Unix filter function which converts geographic longitude and latitude coordinates into cartesian coordinates PaStiX: PaStiX/5.2.2.22-intel-2016.u3 PaStiX (Parallel Sparse matriX package) is a scientific library that provides a high performance parallel solver for very large sparse linear systems based on direct methods. - Homepage: http://pastix.gforge.inria.fr/ Pango: Pango/1.40.0-intel-2016.u3, Pango/1.40.6-foss-2017b, ... Pango is a library for laying out and rendering of text, with an emphasis on internationalization. Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x. - Homepage: http://www.pango.org/ ParMETIS: ParMETIS/3.2.0-goolf-2015a, ParMETIS/3.2.0-intel-2016.u3-test, ... ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes. - Homepage: http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview ParaView: ParaView/5.4.1-spartan_intel-2017.u2-mpi ParaView is a scientific parallel visualizer. Paraview: Paraview/4.4.0-intel-2016.u3, Paraview/5.1.2-intel-2016.u3-mpi, ... Paraview is a scientific parallel visualizer - Homepage: http://www.paraview.org Parse-Yapp: Parse-Yapp/1.05-intel-2016.u3-Perl-5.20.0 A perl frontend to the Parse::Yapp module PartitionFinder: PartitionFinder/1.1.1, PartitionFinder/2.0.0-pre9 Perl: Perl/5.16.3-goolf-2015a, Perl/5.20.0-GCC-4.9.2, ... Larry Wall's Practical Extraction and Report Language - Homepage: http://www.perl.org/ PhyML: PhyML/3.1 Pillow: Pillow/2.8.1-intel-2016.u3-Python-2.7.9, ... Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. PIL is the Python Imaging Library by Fredrik Lundh and Contributors. PoPoolation2: PoPoolation2/1.201 PoPoolation2 allows to compare allele frequencies for SNPs between two or more populations and to identify significant differences. PoPoolation2 requires next generation sequencing data of pooled genomic DNA (Pool-Seq). It may be used for measuring differentiation between populations, for genome wide association studies and for experimental evolution. Polkit: Polkit/0.107-GCC-6.2.0 polkit is an application-level toolkit for defining and handling the policy that allows unprivileged processes to speak to privileged processes: It is a framework for centralizing the decision making process with respect to granting access to privileged operations for unprivileged applications. PopPUNK: PopPUNK/1.1.3-intel-2017.u2-Python-3.6.4 PopPUNK (POPulation Partitioning Using Nucleotide Kmers) Porechop: Porechop/0.2.4-intel-2017.u2-Python-3.6.4 Porechop is a tool for finding and removing adapters from Oxford Nanopore reads. PostgreSQL: PostgreSQL/9.3.5-goolf-2015a, PostgreSQL/9.3.5-intel-2016.u3 PostgreSQL is a powerful, open source object-relational database system. It is fully ACID compliant, has full support for foreign keys, joins, views, triggers, and stored procedures (in multiple languages). It includes most SQL:2008 data types, including INTEGER, NUMERIC, BOOLEAN, CHAR, VARCHAR, DATE, INTERVAL, and TIMESTAMP. It also supports storage of binary large objects, including pictures, sounds, or video. It has native programming interfaces for C/C++, Java, .Net, Perl, Python, Ruby, Tcl, ODBC, among others, and exceptional documentation. Prodigal: Prodigal/2.60-intel-2016.u3 Prodigal (PROkaryotic DynamIc programming Genefinding ALgorithm) is an open source lightweight microbial genefinding program developed at University of Tennessee and Oak Ridge National Laboratory.. Prokka: Prokka/1.13-intel-2016.u3-BioPerl-1.6.924, ... Prokka is a software tool for the rapid annotation of prokaryotic genomes. PyOpenGL: PyOpenGL/3.0.1-intel-2016.u3-Python-2.7.9 PyOpenGL is the most common cross platform Python binding to OpenGL and related APIs. The binding is created using the standard ctypes library, and is provided under an extremely liberal BSD-style Open-Source license. PyQt: PyQt/4.11.4-intel-2016.u3-Python-2.7.9, ... PyQt is a set of Python v2 and v3 bindings for Digia's Qt application framework. PyTables: PyTables/3.4.2-intel-2017.u2-Python-3.6.4 PyTables is a package for managing hierarchical datasets and designed to efficiently and easily cope with extremely large amounts of data. PyTables is built on top of the HDF5 library, using the Python language and the NumPy package. It features an object-oriented interface that, combined with C extensions for the performance-critical parts of the code (generated using Cython), makes it a fast, yet extremely easy to use tool for interactively browse, process and search very large amounts of data. One important feature of PyTables is that it optimizes memory and disk resources so that data takes much less space (specially if on-flight compression is used) than other solutions such as relational or object oriented databases. PyTorch: PyTorch/0.3.1-intel-2017.u2-GCC-5.4.0-CUDA8-Python-3.5.2-GPU, ... PyTorch is a deep learning framework that puts Python first. PyVCF: PyVCF/0.6.8-Python-2.7.10 PyVCF is a VCFv4.0 and 4.1 parser for Python. This is a bundle of PyVCF, which includes dependencies pbr, linecache2, and whatever else comes up. PyYAML: PyYAML/3.12-intel-2017.u2-Python-3.6.4, ... PyYAML is a YAML parser and emitter for the Python programming language. PyZMQ: PyZMQ/14.7.0-intel-2016.u3-Python-2.7.9-zmq3, ... Python bindings for ZeroMQ - Homepage: http://www.zeromq.org/bindings:python Pygments: Pygments/2.0.2-intel-2016.u3-Python-2.7.9 Generic syntax highlighter suitable for use in code hosting, forums, wikis or other applications that need to prettify source code. - Homepage: http://pygments.org/ Pysam: Pysam/0.14-intel-2017.u2-Python-3.6.4, ... Pysam is a python module for reading and manipulating Samfiles. It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix. Python: Python/2.7.9-GCC-4.9.2-bare, Python/2.7.9-GCC-4.9.2, ... Python is a programming language that lets you work more quickly and integrate your systems more effectively. PythonBundle: PythonBundle/2.7.10-intel-2016.u3 Python is a programming language that lets you work more quickly and integrate your systems more effectively. Pyvolve: Pyvolve/0.8.2-intel-2016.u3-Python-2.7.10 Pyvolve is an open-source Python module for simulating sequences along a phylogenetic tree according to continuous-time Markov models of sequence evolution. QIIME: QIIME/1.8.0-intel-2016.u3-Python-2.7.10, ... QIIME consists of native Python 2 code and additionally wraps many external applications. This gives the user flexibility to easily build their own analysis pipelines, making use of popular microbial community analysis tools. QIIME handles the processing of input and output of these applications, so the user can spend time analyzing their data rather than parsing, writing, and converting file formats. QIIME2: QIIME2/2018.2, QIIME2/2019.1-Miniconda3-4.5.4, QIIME2/2019.1 QIIME is an open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data. QUAST: QUAST/4.3-intel-2016.u3, QUAST/4.5-intel-2017.u2 QUAST performs fast and convenient quality evaluation and comparison of genome assemblies. Qhull: Qhull/2015.2-goolf-2015a, Qhull/2015.2-intel-2016.u3 Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, halfspace intersection about a point, furthest-site Delaunay triangulation, and furthest-site Voronoi diagram. The source code runs in 2-d, 3-d, 4-d, and higher dimensions. Qhull implements the Quickhull algorithm for computing the convex hull. Qt: Qt/4.8.2-iomkl-2016.u3, Qt/4.8.6-GCC-4.9.2, Qt/4.8.6-goolf-2015a, ... Qt5: Qt5/5.7.0-intel-2016.u3, Qt5/5.7.0-intel-2017.u2, ... Qt is a comprehensive cross-platform C++ application framework. QuantumESPRESSO: QuantumESPRESSO/5.4.0-intel-2016.u3, ... Quantum ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials (both norm-conserving and ultrasoft). - Homepage: http://www.pwscf.org/ R: R/2.15.3-GCC-4.9.2, R/3.2.1-GCC-4.9.2, R/3.2.1-intel-2016.u3, ... R is a free software environment for statistical computing and graphics. - Homepage: http://www.r-project.org/ R-bundle-Bioconductor: R-bundle-Bioconductor/3.7-GCC-6.2.0-R-3.5.0, ... R is a free software environment for statistical computing and graphics. RAxML: RAxML/7.7.5-intel-2016.u3-hybrid-sse3, ... RNA-SeQC: RNA-SeQC/1.1.8-Java-1.8.0_71 RSEM: RSEM/1.3.1-intel-2017.u2 RNA-Seq by Expectation-Maximization Racon: Racon/1.3.1-GCC-6.2.0, Racon/1.3.1-intel-2016.u3, ... Racon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step. The goal of Racon is to generate genomic consensus which is of similar or better quality compared to the output generated by assembly methods which employ both error correction and consensus steps, while providing a speedup of several times compared to those methods. RapidCFD: RapidCFD/20180426-intel-2017.u2-custom, ... CFD toolbox running on CUDA OpenFOAM solvers ported to Nvidia CUDA. All the calculations are done on the GPU giving a huge speed-up. Still in development stage, waiting for your contribution! Relion: Relion/2.0.3-intel-2016.u3, ... RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a stand-alone computer program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy (cryo-EM). - Homepage: http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page Rmpi: Rmpi/0.6-9-spartan_gcc-6.2.0 An interface (wrapper) to MPI. Roary: Roary/3.12.0-spartan_intel-2017.u2-Perl-5.26.0 Rapid large-scale prokaryote pan genome analysis Rubra: Rubra/20150505-intel-2016.u3-Python-2.7.10 Rubra is a bioinformatics pipeline. Ruby: Ruby/2.4.1-intel-2016.u3 Ruby is a dynamic, open source programming language with a focus on simplicity and productivity. It has an elegant syntax that is natural to read and easy to write. - Homepage: https://www.ruby-lang.org Rust: Rust/1.8.0-goolf-2015a, Rust/1.20.0-goolf-2015a, Rust/1.30.0 Rust is a systems programming language that runs blazingly fast, prevents segfaults, and guarantees thread safety. S-Lang: S-Lang/2.3.0-GCC-4.9.2 S-Lang is a multi-platform programmer's library designed to allow a developer to create robust multi-platform software. It provides facilities required by interactive applications such as display/screen management, keyboard input, keymaps, and so on. SAGE: SAGE/6.4 S.A.G.E. (Statistical Analysis for Genetic Epidemiology) is free software package containing programs for use in the genetic analysis of family, pedigree and individual data. - Homepage: http://darwin.cwru.edu/sage/ SAMblaster: SAMblaster/0.1.22-GCC-4.9.2, SAMblaster/0.1.22-intel-2016.u3 SAMtools: SAMtools/0.1.18-GCC-4.9.2, SAMtools/0.1.18-intel-2016.u3, ... SCALCE: SCALCE/2.7-GCC-4.9.2 SCALCE [skeɪlz] is a FASTQ compression tool that uses locally consistet parsing to obtain better compression rate. SCALCE has been specifically designed for Illumina reads but it can handle other technologies (that generate base pair reads) if the read length is the same throughout the file. SCIP: SCIP/3.2.1-intel-2016.u3 SCIP is currently one of the fastest non-commercial solvers for mixed integer programming (MIP) and mixed integer nonlinear programming (MINLP). It is also a framework for constraint integer programming and branch-cut-and-price. It allows for total control of the solution process and the access of detailed information down to the guts of the solver. - Homepage: http://scip.zib.de/ SCOOP: SCOOP/0.7.1.1-intel-2016.u3-Python-3.5.2 SCOOP (Scalable COncurrent Operations in Python) is a distributed task module allowing concurrent parallel programming on various environments, from heterogeneous grids to supercomputers. SCOTCH: SCOTCH/6.0.0_esmumps-intel-2017.u2, SCOTCH/6.0.4-goolf-2015a, ... Software package and libraries for sequential and parallel graph partitioning, static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning. - Homepage: http://gforge.inria.fr/projects/scotch/ SCons: SCons/2.3.6-GCC-4.9.2-Python-2.7.9, ... SCons is a software construction tool. - Homepage: http://www.scons.org/ SIONlib: SIONlib/1.6.1-goolf-2015a-tools, SIONlib/1.6.1-goolf-2015a SIONlib is a scalable I/O library for parallel access to task-local files. The library not only supports writing and reading binary data to or from several thousands of processors into a single or a small number of physical files, but also provides global open and close functions to access SIONlib files in parallel. This package provides a stripped-down installation of SIONlib for use with performance tools (e.g., Score-P), with renamed symbols to avoid conflicts when an application using SIONlib itself is linked against a tool requiring a different SIONlib version. SIP: SIP/4.16.8-intel-2016.u3-Python-2.7.10, ... SIP is a tool that makes it very easy to create Python bindings for C and C++ libraries. SKESA: SKESA/2.3.0-spartan_intel-2017.u2 SKESA is a de-novo sequence read assembler for cultured single isolate genomes based on DeBruijn graphs. SLEPc: SLEPc/3.6.2-intel-2016.u3-Python-2.7.9, ... SLEPc (Scalable Library for Eigenvalue Problem Computations) is a software library for the solution of large scale sparse eigenvalue problems on parallel computers. It is an extension of PETSc and can be used for either standard or generalized eigenproblems, with real or complex arithmetic. It can also be used for computing a partial SVD of a large, sparse, rectangular matrix, and to solve quadratic eigenvalue problems. - Homepage: http://www.grycap.upv.es/slepc/ SOLAR-Eclipse: SOLAR-Eclipse/8.1.1 SPAdes: SPAdes/3.8.1-GCC-4.9.2-Python-3.5.2, ... Genome assembler for single-cell and isolates data sets SPM: SPM/12-GCC-4.7.4 Statistical Parametric Mapping refers to the construction and assessment of spatially extended statistical processes used to test hypotheses about functional imaging data. These ideas have been instantiated in software that is called SPM. The SPM software package has been designed for the analysis of brain imaging data sequences. The sequences can be a series of images from different cohorts, or time-series from the same subject. The current release is designed for the analysis of fMRI, PET, SPECT, EEG and MEG. - Homepage: http://www.fil.ion.ucl.ac.uk/spm/ SPSS: SPSS/25 SQLite: SQLite/3.8.8.1-GCC-4.9.2, SQLite/3.8.8.1-intel-2016.u3, ... SQLite: SQL Database Engine in a C Library - Homepage: http://www.sqlite.org/ SRA-Toolkit: SRA-Toolkit/2.5.4-centos_linux64, ... The NCBI SRA Toolkit enables reading (dumping) of sequencing files from the SRA database and writing (loading) files into the .sra format STAR: STAR/2.5.3a-intel-2016.u3, STAR/2.6.0c-intel-2018.u4 STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays. - Homepage: https://github.com/alexdobin/STAR SUMO: SUMO/0.31.0-GCC-4.9.2 "Simulation of Urban MObility" (SUMO) is an open source, highly portable, microscopic and continuous road traffic simulation package designed to handle large road networks. - Homepage: http://sumo.dlr.de/wiki/Simulation_of_Urban_MObility_-_Wiki SUNDIALS: SUNDIALS/2.7.0-intel-2016.u3, SUNDIALS/3.1.0-intel-2016.u3 SUNDIALS is a SUite of Nonlinear and DIfferential/ALgebraic equation Solvers. It consists of the following six solvers: CVODE, solves initial value problems for ordinary differential equation (ODE) systems; CVODES, solves ODE systems and includes sensitivity analysis capabilities (forward and adjoint); ARKODE, solves initial value ODE problems with additive Runge-Kutta methods, include support for IMEX methods; IDA, solves initial value problems for differential-algebraic equation (DAE) systems; IDAS, solves DAE systems and includes sensitivity analysis capabilities (forward and adjoint); KINSOL, solves nonlinear algebraic systems. SUPER-FOCUS: SUPER-FOCUS/0.33-intel-2017.u2-Python-3.6.4 A super-fast templating language that borrows the best ideas from the existing templating languages SWASH: SWASH/3.14-intel-2016.u3-mt SWASH is a general-purpose numerical tool for simulating unsteady, non-hydrostatic, free-surface, rotational flow and transport phenomena in coastal waters as driven by waves, tides, buoyancy and wind forces. - Homepage: http://swash.sourceforge.net/ SWIG: SWIG/3.0.11-goolf-2015a-Python-2.7.12, ... SWIG is a software development tool that connects programs written in C and C++ with a variety of high-level programming languages. Sablotron: Sablotron/1.0.3-goolf-2015a Sablotron XML processor - Homepage: http://sablotron.sourceforge.net/ Sagemath: Sagemath/8.1 SageMath is a free open-source mathematics software system licensed under the GPL. It builds on top of many existing open-source packages. Salmon: Salmon/0.11.3 Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data. ScaLAPACK: ScaLAPACK/2.0.2-gompi-2015a-OpenBLAS-0.2.14-LAPACK-3.5.0, ... ScientificPython: ScientificPython/2.9.4-goolf-2015a-Python-2.7.10, ... ScientificPython is a collection of Python modules for scientific computing. It contains support for geometry, mathematical functions, statistics, physical units, IO, visualization, and parallelization. Scipion: Scipion/1.2-GCC-6.2.0-CUDA-9, Scipion/1.2-GCC-6.2.0, ... Scipion is an image processing framework to obtain 3D models of macromolecular complexes using Electron Microscopy. Score-P: Score-P/2.0.1-goolf-2015a The Score-P measurement infrastructure is a highly scalable and easy-to-use tool suite for profiling, event tracing, and online analysis of HPC applications. Seaborn: Seaborn/0.8.1-intel-2017.u2-Python-2.7.11 Seaborn is a Python visualization library based on matplotlib. It provides a high-level interface for drawing attractive statistical graphics. Seqtk: Seqtk/1.3-r106-foss-2017b, Seqtk/1.3-r106-GCCcore-6.4.0, ... Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. Serf: Serf/1.3.8-GCC-4.9.2 The serf library is a high performance C-based HTTP client library built upon the Apache Portable Runtime (APR) library - Homepage: http://serf.apache.org/ Singularity: Singularity/2.5.0-GCC-6.2.0, Singularity/2.5.0-intel-2017.u2, ... Singularity is a portable application stack packaging and runtime utility. Spark: Spark/1.6.2 Sphinx: Sphinx/1.3.3-intel-2016.u3-Python-2.7.9, ... Sphinx is a tool that makes it easy to create intelligent and beautiful documentation. It was originally created for the new Python documentation, and it has excellent facilities for the documentation of Python projects, but C/C++ is already supported as well, and it is planned to add special support for other languages as well. - Homepage: http://sphinx.pocoo.org/ Spidermonkey: Spidermonkey/1.0.0-GCC-6.2.0 SpiderMonkey is Mozilla's JavaScript engine written in C and C++. It is used in various Mozilla products, including Firefox, and is available under the MPL2. Stacks: Stacks/2.3-spartan_gcc-6.2.0 Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population genomics and phylogeography. Stata: Stata/12, Stata/15 Stata is a complete, integrated statistical software package that provides everything you need for data analysis, data management, and graphics. - Homepage: http://www.stata.com/support/updates/ StringTie: StringTie/1.3.3b-intel-2016.u3 StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus. - Homepage: https://ccb.jhu.edu/software/stringtie/#contact Structure: Structure/2.3.4-intel-2016.u3 Subread: Subread/1.5.1-GCC-4.9.2, Subread/1.6.3-GCC-8.2.0, ... Subversion: Subversion/1.8.14-GCC-4.9.2 Subversion is an open source version control system. - Homepage: http://subversion.apache.org/ SuiteSparse: SuiteSparse/3.7.1-spartan_intel-2017.u2-ParMETIS-4.0.3, ... SuiteSparse is a collection of libraries manipulate sparse matrices. Summovie: Summovie/1.0.2 Use with Unlur. Unblur is used to align the frames of movies recorded on an electron microscope to reduce image blurring due to beam-induced motion. - Homepage: http://grigoriefflab.janelia.org/unblur Szip: Szip/2.1-foss-2017b, Szip/2.1-GCC-4.9.2, Szip/2.1-GCC-5.4.0, ... TAU: TAU/2.27-goolf-2015a, TAU/2.27.1-goolf-2015a, TAU/2.27.2-goolf-2015a The TAU Performance System is a portable profiling and tracing toolkit for performance analysis of parallel programs written in Fortran, C, C++, Java, Python. Tcl: Tcl/8.5.7-GCC-4.9.3, Tcl/8.5.12-GCC-6.2.0, Tcl/8.5.12-intel-2016.u3, ... Tensorflow: Tensorflow/0.12.0-intel-2017.u2-Python-2.7.13-GPU, ... An open-source software library for Machine Intelligence Theano: ... Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently. Thunar: Thunar/1.6.11-intel-2016.u3 Thunar is the Xfce file manager, a GTK+ 2 GUI to organise the files on your computer. - Homepage: xfce.org Tk: Tk/8.5.12-intel-2016.u3, Tk/8.6.3-GCC-4.9.2-no-X11, ... Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building a graphical user interface (GUI) in many different programming languages. - Homepage: http://www.tcl.tk/ Tkinter: Tkinter/2.7.11-intel-2017.u2-Python-2.7.11, ... Tkinter module, built with the Python buildsystem TopHat: TopHat/2.1.0-intel-2016.u3, TopHat/2.1.1-GCC-4.9.2, ... Torch: Torch/20171208-cuDNN7-intel-2017.u2-GCC-5.4.0-CUDA8, ... Torch is a scientific computing framework with wide support for machine learning algorithms that puts GPUs first. It is easy to use and efficient, thanks to an easy and fast scripting language, LuaJIT, and an underlying C/CUDA implementation. Trilinos: Trilinos/12.4.2-intel-2016.u3-Python-2.7.11 TrimGalore: TrimGalore/0.4.4 Trim Galore! is a wrapper script to automate quality and adapter trimming as well as quality control, with some added functionality to remove biased methylation positions for RRBS sequence files (for directional, non-directional (or paired-end) sequencing). Trim_Galore: Trim_Galore/0.4.4-intel-2016.u3, ... A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries. Trimmomatic: Trimmomatic/0.30, Trimmomatic/0.36-Java-1.8.0_71, ... Trinity: Trinity/2.6.6-intel-2017.u2 Trinity represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-Seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-Seq reads. TrinityRNAseq: TrinityRNAseq/2.5.1-intel-2017.u2 TurboVNC: TurboVNC/2.1.1-intel-2016.u3, TurboVNC/2.1.1-intel-2017.u2 TurboVNC is a high-performance, enterprise-quality version of VNC based on TightVNC, TigerVNC, and X.org . It contains a variant of Tight encoding that is tuned for maximum performance and compression with 3D applications (VirtualGL), video, and other image-intensive workloads. TurboVNC, in combination with VirtualGL, provides a complete solution for remotely displaying 3D applications with interactive performance. Please use TurboVNC server in interactive sessions (`sinteractive`) only. Note that tunnelling will be required for this. - Homepage: https://sourceforge.net/projects/turbovnc/ UDUNITS: UDUNITS/2.2.20-intel-2016.u3, UDUNITS/2.2.26-GCC-4.9.2, ... UDUNITS supports conversion of unit specifications between formatted and binary forms, arithmetic manipulation of units, and conversion of values between compatible scales of measurement. - Homepage: http://www.unidata.ucar.edu/software/udunits/ UFL: UFL/1.6.0-intel-2016.u3-Python-2.7.9, ... The Unified Form Language (UFL) is a domain specific language for declaration of finite element discretizations of variational forms. More precisely, it defines a flexible interface for choosing finite element spaces and defining expressions for weak forms in a notation close to mathematical notation. - Homepage: https://launchpad.net/ufl Unblur: Unblur/1.0.2 Unblur is used to align the frames of movies recorded on an electron microscope to reduce image blurring due to beam-induced motion. - Homepage: http://grigoriefflab.janelia.org/unblur VCFtools: VCFtools/0.1.12-GCC-4.9.2-Perl-5.20.0, ... VMD: VMD/1.9.1, VMD/1.9.3 VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VTK: VTK/6.3.0-intel-2016.u3-test, VTK/6.3.0-intel-2016.u3-Python-2.7.9, ... Valgrind: Valgrind/3.9.0-GCC-4.9.2, Valgrind/3.10.0-GCC-4.9.2, ... Valgrind: Debugging and profiling tools - Homepage: http://valgrind.org/downloads/ Velvet: Velvet/1.2.10-GCC-4.9.2-mt-kmer_57, ... ViennaRNA: ViennaRNA/2.1.3-GCC-4.9.2, ViennaRNA/2.1.3-GCC-4.9.3 Software and Documents from the Theoretical Biochemistry Institute, University of Vienna Voro++: Voro++/0.4.6-GCC-6.2.0, ... Voro++ is a software library for carrying out three-dimensional computations of the Voronoi tessellation. A distinguishing feature of the Voro++ library is that it carries out cell-based calculations, computing the Voronoi cell for each particle individually. It is particularly well-suited for applications that rely on cell-based statistics, where features of Voronoi cells (eg. volume, centroid, number of faces) can be used to analyze a system of particles. Vt: Vt/0.5772-spartan_gcc-6.2.0 vt is a variant tool set that discovers short variants from Next Generation Sequencing data. WRF: WRF/3.6.1-intel-2016.u3-dmpar The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale numerical weather prediction system designed to serve both operational forecasting and atmospheric research needs. - Homepage: http://www.wrf-model.org Wine: Wine/1.8.6, Wine/4.0.0-GCC-6.2.0 Wine: Free implementation of Windows on Unix - Homepage: http://www.winehq.com/ X11: X11/20160819-GCC-4.9.2, X11/20160819-GCC-6.2.0, ... The X Window System (X11) is a windowing system for bitmap displays X11-Applications: X11-Applications/20160819-intel-2016.u3 The X Window System (X11) is a windowing system for bitmap displays XKeyboardConfig: XKeyboardConfig/2.16-intel-2016.u3-Python-2.7.11, ... The non-arch keyboard configuration database for X Window. The goal is to provide the consistent, well-structured, frequently released open source of X keyboard configuration data for X Window System implementations (free, open source and commercial). The project is targeted to XKB-based systems. - Homepage: http://www.freedesktop.org/wiki/Software/XKeyboardConfig/ XML-LibXML: XML-LibXML/2.0132-spartan_intel-2017.u2-Perl-5.26.0 Perl binding for libxml2 XML-Parser: XML-Parser/2.41-GCC-4.9.2-Perl-5.20.0, ... This is a Perl extension interface to James Clark's XML parser, expat. XML-Writer: XML-Writer/0.625-intel-2016.u3-Perl-5.20.0 Perl extension for writing XML documents. XOP: XOP/2.4 XOP provides a set of codes from different authors and written in different computer languages for modeling of x-ray radiation sources and their interaction with x-ray optical components such as mirrors, filters, and multilayers and offers a variety of analyses and data visualizations. XSD: XSD/4.0.0-intel-2016.u3 CodeSynthesis XSD is an open-source, cross-platform W3C XML Schema to C++ data binding compiler. Provided with an XML instance specification (XML Schema), it generates C++ classes that represent the given vocabulary as well as XML parsing and serialization code. XZ: XZ/5.2.2-foss-2017b, XZ/5.2.2-GCC-4.6.4, XZ/5.2.2-GCC-4.9.2, ... xz: XZ utilities - Homepage: http://tukaani.org/xz/ Xerces-C++: Xerces-C++/3.1.1-GCC-4.9.2, Xerces-C++/3.1.1-intel-2016.u3 Xerces-C++ is a validating XML parser written in a portable subset of C++. Xerces-C++ makes it easy to give your application the ability to read and write XML data. A shared library is provided for parsing, generating, manipulating, and validating XML documents using the DOM, SAX, and SAX2 APIs. - Homepage: http://xerces.apache.org/xerces-c/ Xpress: Xpress/Xpress-7.9 FICO Xpress is the premier mathematical modeling and optimization software suite - Homepage: http://www.fico.com/en/products/fico-xpress-optimization Yambo: Yambo/3.4.2-intel-2016.u3 Yambo is a FORTRAN/C code for Many-Body calculations in solid state and molecular physics. Yambo relies on the Kohn-Sham wavefunctions generated by two DFT public codes: abinit, and PWscf. - Homepage: http://www.yambo-code.org Yasm: Yasm/1.3.0-GCC-4.9.2, Yasm/1.3.0-intel-2016.u3, ... Yasm: Complete rewrite of the NASM assembler with BSD license ZeroMQ: ZeroMQ/3.2.5-intel-2016.u3, ZeroMQ/4.2.5-intel-2016.u3 ZeroMQ looks like an embeddable networking library but acts like a concurrency framework. It gives you sockets that carry atomic messages across various transports like in-process, inter-process, TCP, and multicast. You can connect sockets N-to-N with patterns like fanout, pub-sub, task distribution, and request-reply. It's fast enough to be the fabric for clustered products. Its asynchronous I/O model gives you scalable multicore applications, built as asynchronous message-processing tasks. It has a score of language APIs and runs on most operating systems. - Homepage: http://www.zeromq.org/ abacas: abacas/1.3.1 ant: ant/1.10.0-Java-1.8.0_71, ant/1.10.2-Java-9.0.4 Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications. - Homepage: http://ant.apache.org/ apex: apex/0.1-intel-2017.u2-Python-3.6.4 This repository holds NVIDIA-maintained utilities to streamline mixed precision and distributed training in Pytorch. Some of the code here will be included in upstream Pytorch eventually. The intention of Apex is to make up-to-date utilities available to users as quickly as possible. arpack-ng: arpack-ng/3.3.0-intel-2016.u3, arpack-ng/3.3.0-iompi-2016.u3, ... ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems. - Homepage: http://forge.scilab.org/index.php/p/arpack-ng/ at-spi2-atk: at-spi2-atk/2.30.0-intel-2017.u2 GTK+ module for bridging AT-SPI to ATK at-spi2-core: at-spi2-core/2.30.0-intel-2017.u2, ... GTK+ module for bridging AT-SPI to ATK awscli: awscli/1.16.67-GCC-6.2.0 Universal Command Line Interface for Amazon Web Services bcl2fastq2: bcl2fastq2/2-20-0 beagle-lib: beagle-lib/2.1.2-GCC-4.9.2, beagle-lib/2.1.2-goolf-2015a, ... binutils: binutils/2.25-foss-2017b-binutils-2.25, ... binutils: GNU binary utilities - Homepage: http://directory.fsf.org/project/binutils/ biobambam: biobambam/0.0.99-intel-2016.u3 blasr: blasr/smrtanalysis-2.1-GCC-4.9.2 BLASR (Basic Local Alignment with Successive Refinement) rapidly maps reads to genomes by finding the highest scoring local alignment or set of local alignments between the read and the genome. Optimized for PacBio's extraordinarily long reads and taking advantage of rich quality values, BLASR maps reads rapidly with high accuracy. blobtools: blobtools/0.9.19.4-intel-2016.u3 Blobtools is a tool set for the visualisation of (draft) genome assemblies using TAGC (Taxon-annotated Gc-Coverage) plots Kumar et al. 2012. bmvdgeijn-WASP: bmvdgeijn-WASP/0.3.3-intel-2017.u2-Python-3.6.4 WASP is a suite of tools for unbiased allele-specific read mapping and discovery of molecular QTLs. botocore: botocore/1.12.58-GCC-6.2.0 Universal Command Line Interface for Amazon Web Services bzip2: bzip2/1.0.6-foss-2017b, bzip2/1.0.6-GCC-4.9.2, ... cMESS: cMESS/1.0.0-spartan_intel-2017.u2-Python-2.7.13 M.E.S.S. is the successor to the LyaPack Toolbox for MATLAB. It is intended for solving large sparse matrix equations. cURL: cURL/7.43.0-GCC-4.9.2, cURL/7.43.0-GCC-5.4.0, ... cairo: cairo/1.12.18-GCC-4.9.2, cairo/1.12.18-intel-2016.u3, ... capnproto: capnproto/0.5.3-GCC-4.9.2 The Cap’n Proto tools, including the compiler (which takes .capnp files and generates source code for them), are written in C++. Therefore, you must install the C++ package even if your actual development language is something else. cddlib: cddlib/0.94-GCC-4.9.2 The C-library cddlib is a C implementation of the Double Description Method of Motzkin et al. centrifuge: centrifuge/1.0.3b-intel-2016.u3, ... [Centrifuge] is a novel microbial classification engine that enables rapid, accurate and sensitive labeling of reads and quantification of species on desktop computers. clustalw: clustalw/2.1-intel-2016.u3 Multiple alignment of nucleic acid and protein sequences concoct: concoct/0.4.0-intel-2017.u2-Python-2.7.11 The Cython language makes writing C extensions for the Python language as easy as Python itself. Cython is a source code translator based on the well-known Pyrex, but supports more cutting edge functionality and optimizations. cosi2: cosi2/2.02-GCC-4.9.2, cosi2/2.3.0rc4-GCC-4.9.2 cosi2 is an efficient coalescent simulator with support for selection, population structure, variable recombination rates, and gene conversion. It supports exact and approximate simulation modes. cromwell: cromwell/31-Java-1.8.0_71 Cromwell is a Workflow Management System geared towards scientific workflows. cuDNN: cuDNN/5.1-CUDA-8.0.44, cuDNN/5.1-intel-2017.u2-CUDA-8.0.44, ... The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for deep neural networks. - Homepage: https://developer.nvidia.com/cudnn cub: cub/1.6.4 NVLabs CUB provides state-of-the-art, reusable software components for every layer of the CUDA programming model - Homepage: https://nvlabs.github.io/cub/ cutadapt: cutadapt/1.13-intel-2016.u3-Python-2.7.12, ... cutadapt removes adapter sequences from high-throughput sequencing data. This is usually necessary when the read length of the sequencing machine is longer than the molecule that is sequenced, for example when sequencing microRNAs. dbus-glib: dbus-glib/0.106-GCC-6.2.0, dbus-glib/0.108-intel-2016.u3, ... D-Bus is a message bus system, a simple way for applications to talk to one another. deepTools: deepTools/3.1.2-intel-2017.u2-Python-3.6.4 deepTools is a suite of python tools particularly developed for the efficient analysis of high-throughput sequencing data, such as ChIP-seq, RNA-seq or MNase-seq. diamond: diamond/0.9.10 DIAMOND is a sequence aligner for protein and translated DNA searches and functions as a drop-in replacement for the NCBI BLAST software tools. It is suitable for protein-protein search as well as DNA-protein search on short reads and longer sequences including contigs and assemblies, providing a speedup of BLAST ranging up to x20,000. dsk: dsk/2.2.0-GCC-4.9.2, dsk/2.2.0-GCC-4.9.3 DSK is a k-mer counter for reads or genomes. duck: duck/6.8.3.29107 duck is a WebDAV client. dx-toolkit: dx-toolkit/0.168.0-Python-2.7.9 The DNAnexus Platform SDK (a.k.a. dx-toolkit) includes the dx command-line client, tools for building and debugging apps, and other utilities for working with DNA data on the platform. ea-utils: ea-utils/r805-GCC-4.8.1, ea-utils/r805-GCC-4.9.2, ... Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more. easyspin: easyspin/5.2.21-intel-2017.u2, easyspin/5.2.21 EasySpin is a MATLAB toolbox for simulating and fitting a wide range of Electron Paramagnetic Resonance (EPR) spectra. It supplements the numerical and visualization power of MATLAB with the best computational methods devised by EPR spectroscopists. eudev: eudev/3.1.2-GCC-4.9.2, eudev/3.1.2-goolf-2015a, ... eudev is a fork of systemd-udev with the goal of obtaining better compatibility with existing software such as OpenRC and Upstart, older kernels, various toolchains and anything else required by users and various distributions. - Homepage: https://wiki.gentoo.org/wiki/Project:Eudev exo: exo/0.10.3-intel-2016.u3 - Homepage: https://xfce.org/ expat: expat/2.1.0-foss-2017b, expat/2.1.0-GCC-4.9.2, ... faiss: faiss/1.4.0-intel-2017.u2-GCC-6.2.0-CUDA9, ... Faiss is a library for efficient similarity search and clustering of dense vectors. It is developed by Facebook AI Research. fastGEAR: fastGEAR/16Dec2016, fastGEAR/20161216 fastqc: fastqc/0.11.3, fastqc/0.11.5 file: file/5.35-spartan_intel-2017.u2 The file command is 'a file type guesser', that is, a command-line tool that tells you in words what kind of data a file contains. fixesproto: fixesproto/5.0-GCC-4.9.2, fixesproto/5.0-goolf-2015a, ... X.org FixesProto protocol headers. - Homepage: http://www.freedesktop.org/wiki/Software/xlibs flex: flex/2.5.35-GCC-4.9.2, flex/2.5.35-intel-2016.u3, ... Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, sometimes called a tokenizer, is a program which recognizes lexical patterns in text. fontconfig: fontconfig/2.11.1-GCC-4.9.2, fontconfig/2.11.1-goolf-2015a, ... fontsproto: fontsproto/2.1.3-GCC-4.9.2, fontsproto/2.1.3-goolf-2015a, ... X11 font extension wire protocol - Homepage: http://www.freedesktop.org/wiki/Software/xlibs foss: foss/2017b GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK. freebayes: freebayes/1.2.0-foss-2017b Bayesian haplotype-based polymorphism discovery and genotyping. freeglut: freeglut/2.8.1-goolf-2015a, freeglut/2.8.1-intel-2016.u3, ... freeglut is a completely OpenSourced alternative to the OpenGL Utility Toolkit (GLUT) library. - Homepage: http://freeglut.sourceforge.net/ freetype: freetype/2.5.3-GCC-4.9.2, freetype/2.5.5-foss-2017b, ... FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display servers, font conversion tools, text image generation tools, and many other products as well. fsm-lite: fsm-lite/1.0-spartan_intel-2017.u2 A singe-core implemetation of frequency-based substring mining. future: future/0.16.0-spartan_intel-2017.u2-Python-2.7.13 This library is the reference implementation of the Python wheel packaging standard, as defined in PEP 427. fxtract: fxtract/2.3-GCC-4.9.4 Extract sequences from a fastx (fasta or fastq) file given a subsequence. g2clib: g2clib/1.6.0-spartan_intel-2017.u2 Library contains GRIB2 encoder/decoder ('C' version). g2lib: g2lib/1.4.0-spartan_intel-2017.u2 Library contains GRIB2 encoder/decoder and search/indexing routines. garcon: garcon/0.4.0-intel-2016.u3 - Homepage: https://xfce.org/ gatb-core: gatb-core/1.1.0, gatb-core/1.2.1, gatb-core/1.3.0 Genome Analysis Toolbox with de-Bruijn graph gcccuda: gcccuda/2017.01 GNU Compiler Collection (GCC) based compiler toolchain, along with CUDA toolkit. gdrcopy: gdrcopy/1.3-PGI-18.7-GCC-6.4.0-2.28, ... A low-latency GPU memory copy library based on NVIDIA GPUDirect RDMA technology. gettext: gettext/0.19.2-foss-2017b, gettext/0.19.2-GCC-4.6.4, ... GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation - Homepage: http://www.gnu.org/software/gettext/ gflags: gflags/2.1.2-GCC-4.9.2, gflags/2.1.2-intel-2016.u3, ... git: git/1.8.5.6-GCC-4.9.2, git/2.10.0-GCC-4.9.2, git/2.19.1-GCC-6.2.0 glibmm: glibmm/2.46.1-intel-2017.u2-GCC-6.2.0-CUDA9, ... This is glibmm, a C++ API for parts of glib that are useful for C++. glog: glog/0.3.4-GCC-4.9.2, glog/0.3.4-intel-2016.u3, ... glproto: glproto/1.4.16-GCC-4.9.2, glproto/1.4.16-goolf-2015a, ... gmsh: gmsh/3.0.6 gmsh is a 3D finite element mesh generator with a build-in CAD engine and post-processor. gnuplot: gnuplot/5.0.0-foss-2017b, gnuplot/5.0.0-GCC-4.9.2, ... gompi: gompi/GCC-4.6.4-OpenMPI-1.8.4, gompi/GCC-6.2.0-OpenMPI-3.0.0, ... gompic: gompic/2017.01 GNU Compiler Collection (GCC) based compiler toolchain along with CUDA toolkit, including OpenMPI for MPI support with CUDA features enabled. goolf: goolf/2015a goolfc: goolfc/2017.01 GCC based compiler toolchain __with CUDA support__, and including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK. gperf: gperf/3.0.4-foss-2017b, gperf/3.0.4-GCC-4.9.2, ... GNU gperf is a perfect hash function generator. For a given list of strings, it produces a hash function and hash table, in form of C or C++ code, for looking up a value depending on the input string. The hash function is perfect, which means that the hash table has no collisions, and the hash table lookup needs a single string comparison only. - Homepage: http://www.gnu.org/software/gperf/ grace: grace/5.1.25-intel-2016.u3 Grace is a WYSIWYG 2D plotting tool for X Windows System and Motif. - Homepage: http://freecode.com/projects/grace gretl: gretl/2018c-GCC-6.2.0-LAPACK-3.8.0-OpenBLAS-0.3.5 A cross-platform software package for econometric analysis. gtk-xfce-engine: gtk-xfce-engine/2.10.0-intel-2016.u3 - Homepage: http:/xfce.org/ gzip: gzip/1.8-goolf-2015a gzip (GNU zip) is a popular data compression program as a replacement for compress gzstream: gzstream/1.5-GCC-4.9.2, gzstream/1.5-intel-2016.u3 Gzstream is a small C++ library, basically just a wrapper, that provides the functionality of the zlib C-library in a C++ iostream. h2o4gpu: h2o4gpu/0.2.0-intel-2017.u2-GCC-6.2.0-CUDA9-Python-3.6.4-GPU An open-source software library for Machine Intelligence hdbscan: hdbscan/0.8.18-intel-2017.u2-Python-3.6.4 Hierarchical Density-Based Spatial Clustering of Applications with Noise. Performs DBSCAN over varying epsilon values and integrates the result to find a clustering that gives the best stability over epsilon. This allows HDBSCAN to find clusters of varying densities (unlike DBSCAN), and be more robust to parameter selection. help2man: help2man/1.47.4-GCCcore-6.3.0, help2man/1.47.4-GCCcore-6.4.0, ... help2man produces simple manual pages from the '--help' and '--version' output of other commands. hwloc: hwloc/1.10.0-GCC-4.9.2, hwloc/1.10.1-GCC-4.6.4, ... The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various system attributes such as cache and memory information as well as the locality of I/O devices such as network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering information about modern computing hardware so as to exploit it accordingly and efficiently. iCP: iCP/1.4 interface Comsol PhreeqC icc: icc/2016.u3-GCC-4.9.2, icc/2017.u2-GCC-5.4.0, icc/2017.u2-GCC-6.2.0, ... iccifort: iccifort/2016.u3-GCC-4.9.2, iccifort/2017.u2-GCC-5.4.0, ... iccifortcuda: iccifortcuda/2018.u4-GCC-8.2.0 Intel C, C++ & Fortran compilers with CUDA toolkit iceauth: iceauth/1.0.5-intel-2016.u3 - Homepage: http://www.x.org ifort: ifort/2016.u3-GCC-4.9.2, ifort/2017.u2-GCC-5.4.0, ... iimpi: iimpi/2016.u3-GCC-4.9.2, iimpi/2017.u2-GCC-5.4.0, ... Intel C/C++ and Fortran compilers, alongside Intel MPI. imake: imake/1.0.5-goolf-2015a imake is a Makefile-generator that is intended to make it easier to develop software portably for multiple systems. - Homepage: http://www.x.org/ imkl: imkl/11.3.3.210-iimpi-2016.u3-GCC-4.9.2, ... Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more. impi: impi/5.1.3.223-iccifort-2016.u3-GCC-4.9.2, ... The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification. inputproto: inputproto/2.3.1-GCC-4.9.2, inputproto/2.3.1-GCC-6.2.0, ... X.org InputProto protocol headers. - Homepage: http://www.freedesktop.org/wiki/Software/xlibs intel: intel/2016.u3-GCC-4.9.2-CUDA7.5, intel/2016.u3, ... Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL. intltool: intltool/0.51.0-GCC-4.9.2, ... intltool is a set of tools to centralize translation of many different file formats using GNU gettext-compatible PO files. iomkl: iomkl/2016.u3 Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & OpenMPI. - Homepage: http://software.intel.com/en-us/intel-cluster-toolkit-compiler/ iomklc: iomklc/2018.u4 Intel Cluster Toolchain Compiler Edition Intel C/C++ and Fortran compilers, Intel MKL, plus nVidia CUDA. With added OpenMPI, ucx tuned for Spartan's gpgpu cluster. iompi: iompi/spartan_intel, iompi/2016.u3, iompi/2017.u2-cuda9.1, ... Toolchain with Intel C, C++ and Fortran compilers, alongside OpenMPI. - Homepage: http://software.intel.com/en-us/intel-cluster-toolkit-compiler/ iompic: iompic/2018.u4 Intel C/C++ and Fortran compilers, alongside Open MPI. iqtree: iqtree/1.4.2, iqtree/1.5.0a, iqtree/1.5.1-intel-2016.u3, ... Efficient phylogenomic software by maximum likelihood joe: joe/4.6 JOE is a full featured terminal-based screen editor. jsonschema: jsonschema/2.6.0-intel-2017.u2-Python-3.6.4 Python plotting library for collaborative, interactive, publication-quality graphs. kWIP: kWIP/0.2.0-intel-2016.u3 The k-mer Weighted Inner Product. kbproto: kbproto/1.0.6-GCC-4.9.2, kbproto/1.0.6-GCC-6.2.0, ... X.org KBProto protocol headers. - Homepage: http://www.freedesktop.org/wiki/Software/xlibs kentUtils: kentUtils/302.1.0-GCC-4.9.2 khmer: khmer/2.0-intel-2016.u3-Python-2.7.10 The khmer software is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. lasagne: ... Lasagne is a lightweight library to build and train neural networks in Theano leveldb: leveldb/1.19-GCC-4.9.2, leveldb/1.19-intel-2016.u3, ... LevelDB is a fast key-value storage library written at Google that provides an ordered mapping from string keys to string values. - Homepage: https://github.com/google/leveldb/ libGLU: libGLU/9.0.0-GCC-4.9.2, libGLU/9.0.0-GCC-6.2.0-Mesa-17.2.8, ... The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. - Homepage: ftp://ftp.freedesktop.org/pub/mesa/glu/ libICE: libICE/1.0.9-GCC-6.2.0, libICE/1.0.9-goolf-2015a, ... X Inter-Client Exchange library for freedesktop.org libSM: libSM/1.2.2-GCC-6.2.0, libSM/1.2.2-goolf-2015a, ... X11 Session Management library, which allows for applications to both manage sessions, and make use of session managers to save and restore their state for later use. libX11: libX11/1.6.3-GCC-4.9.2-Python-2.7.9, ... X11 client-side library libXau: libXau/1.0.8-GCC-4.9.2, libXau/1.0.8-GCC-6.2.0, ... The libXau package contains a library implementing the X11 Authorization Protocol. This is useful for restricting client access to the display. - Homepage: http://www.freedesktop.org/wiki/Software/xlibs libXaw: libXaw/1.0.12-goolf-2015a libXaw provides the Athena Widgets toolkit - Homepage: http://www.freedesktop.org/wiki/Software/xlibs libXcursor: libXcursor/1.1.14-intel-2016.u3, ... X Cursor management library - Homepage: http://www.freedesktop.org/wiki/Software/xlibs libXdamage: libXdamage/1.1.4-GCC-4.9.2, libXdamage/1.1.4-goolf-2015a, ... X Damage extension library - Homepage: http://www.freedesktop.org/wiki/Software/xlibs libXdmcp: libXdmcp/1.1.2-GCC-4.9.2, libXdmcp/1.1.2-GCC-6.2.0, ... The libXdmcp package contains a library implementing the X Display Manager Control Protocol. This is useful for allowing clients to interact with the X Display Manager. - Homepage: http://www.freedesktop.org/wiki/Software/xlibs libXext: libXext/1.3.3-GCC-4.9.2, libXext/1.3.3-GCC-6.2.0, ... Common X Extensions library - Homepage: http://www.freedesktop.org/wiki/Software/xlibs libXfixes: libXfixes/5.0.1-GCC-4.9.2, libXfixes/5.0.1-goolf-2015a, ... X Fixes extension library - Homepage: http://www.freedesktop.org/wiki/Software/xlibs libXfont: libXfont/1.5.1-GCC-4.9.2-Python-2.7.9, ... X font libary - Homepage: http://www.freedesktop.org/wiki/Software/xlibs libXft: libXft/2.3.2-GCC-4.9.2, libXft/2.3.2-GCC-6.2.0, ... libXi: libXi/1.7.4-goolf-2015a, libXi/1.7.4-intel-2016.u3-Python-2.7.11, ... LibXi provides an X Window System client interface to the XINPUT extension to the X protocol. - Homepage: http://www.freedesktop.org/wiki/Software/xlibs libXinerama: libXinerama/1.1.3-intel-2016.u3, ... Xinerama multiple monitor library - Homepage: http://www.freedesktop.org/wiki/Software/xlibs libXmu: libXmu/1.1.2-goolf-2015a, libXmu/1.1.2-intel-2016.u3 libXmu provides a set of miscellaneous utility convenience functions for X libraries to use. libXmuu is a lighter-weight version that does not depend on libXt or libXext - Homepage: http://www.freedesktop.org/wiki/Software/xlibs libXp: libXp/1.0.3-intel-2016.u3, libXp/1.0.3-spartan_intel-2017.u2 libXp provides the X print library. - Homepage: http://www.freedesktop.org/wiki/Software/xlibs libXpm: libXpm/3.5.11-goolf-2015a, libXpm/3.5.11-intel-2016.u3 libXp provides the X print library. - Homepage: http://www.freedesktop.org/wiki/Software/xlibs libXrandr: libXrandr/1.5.0-intel-2016.u3, libXrandr/1.5.0-intel-2017.u2 X Resize, Rotate and Reflection extension library - Homepage: http://www.freedesktop.org/wiki/Software/xlibs libXrender: libXrender/0.9.9-intel-2016.u3-Python-2.7.9, ... X11 client-side library - Homepage: http://www.freedesktop.org/wiki/Software/xlibs libXt: libXt/1.1.5-goolf-2015a, libXt/1.1.5-intel-2016.u3-Python-2.7.9, ... libXt provides the X Toolkit Intrinsics, an abstract widget library upon which other toolkits are based. Xt is the basis for many toolkits, including the Athena widgets (Xaw), and LessTif (a Motif implementation). - Homepage: http://www.freedesktop.org/wiki/Software/xlibs libXtst: libXtst/1.2.2-intel-2017.u2, libXtst/1.2.3-intel-2018.u4 Client library for X Record and Test extensions. libXxf86vm: libXxf86vm/1.1.4-GCC-6.2.0 X11 XFree86 video mode extension library libcanberra: libcanberra/0.30-GCC-6.2.0, libcanberra/0.30-intel-2016.u3, ... libdap: libdap/3.19.1-intel-2016.u3, libdap/3.19.1-intel-2017.u2 A C++ SDK which contains an implementation of DAP 2.0 and the development versions of DAP3, up to 3.4. This includes both Client- and Server-side support classes. libdrm: libdrm/2.4.27-GCC-4.9.2, libdrm/2.4.27-intel-2016.u3, ... libelf: libelf/0.8.13-GCC-4.9.2 libepoxy: libepoxy/1.4.3-intel-2016.u3, libepoxy/1.4.3-intel-2017.u2, ... Epoxy is a library for handling OpenGL function pointer management for you libexif: libexif/0.6.21-intel-2016.u3 The libexif package contains a library for parsing, editing, and saving EXIF data. Most digital cameras produce EXIF files, which are JPEG files with extra tags that contain information about the image. All EXIF tags described in EXIF standard 2.1 are supported. - Homepage: http://libexif.sourceforge.net/ libffcall: libffcall/1.13-GCC-6.2.0, libffcall/1.13-GCCcore-6.4.0 GNU Libffcall is a collection of four libraries which can be used to build foreign function call interfaces in embedded interpreters libffi: libffi/3.1-intel-2016.u3, libffi/3.1-iomkl-2016.u3, ... The libffi library provides a portable, high level programming interface to various calling conventions. This allows a programmer to call any function specified by a call interface description at run-time. - Homepage: http://sourceware.org/libffi/ libfontenc: libfontenc/1.1.3-GCC-4.9.2, libfontenc/1.1.3-goolf-2015a, ... X11 font encoding library - Homepage: http://www.freedesktop.org/wiki/Software/xlibs/ libgd: libgd/2.1.0-GCC-4.9.2, libgd/2.1.0-intel-2016.u3, ... libgladeui: libgladeui/3.8.5-intel-2016.u3GTK+2 - Homepage: https://glade.gnome.org libgpuarray: libgpuarray/0.7.6-intel-2017.u2-GCC-6.2.0-CUDA9-Python-3.5.2, ... Library to manipulate tensors on the GPU. libgtextutils: libgtextutils/0.6.1-intel-2016.u3 libgudev: libgudev/230-intel-2016.u3 libgudev is a library with GObject bindings to libudev - Homepage: https://wiki.gnome.org/Projects/libgudev libharu: libharu/2.2.0-intel-2016.u3, libharu/2.3.0-spartan_intel-2017.u2 libidn: libidn/1.34-GCC-8.2.0, libidn/1.34-intel-2016.u3, ... GNU Libidn is a fully documented implementation of the Stringprep, Punycode and IDNA specifications. Libidn's purpose is to encode and decode internationalized domain names. libjpeg: libjpeg/9c-intel-2016.u3 This package contains C software to implement JPEG image encoding, decoding, and transcoding. JPEG is a standardized compression method for full-color and grayscale images. libjpeg-turbo: libjpeg-turbo/1.4.0-foss-2017b, ... libmaus: libmaus/0.0.99-intel-2016.u3 libmaus2: libmaus2/2.0.9-intel-2016.u3 libmng: libmng/2.0.3-intel-2016.u3 libmng -THE reference library for reading, displaying, writing and examining Multiple-Image Network Graphics. MNG is the animation extension to the popular PNG image-format. - Homepage: https://sourceforge.net/projects/libmng/ libogg: libogg/1.3.2-GCC-6.2.0, libogg/1.3.2-intel-2016.u3, ... libpciaccess: libpciaccess/0.13.1-GCC-4.9.2, ... libpng: libpng/1.6.6-goolf-2015a, libpng/1.6.12-GCC-4.9.2, ... libpng is the official PNG reference library libpthread-stubs: libpthread-stubs/0.3-GCC-4.9.2, ... libreadline: libreadline/6.3-GCC-4.6.4, libreadline/6.3-GCC-4.9.2, ... libsigc++: libsigc++/2.6.1-intel-2017.u2-GCC-6.2.0-CUDA9, ... libsigc++ implements a typesafe callback system for standard C++. It allows you to define signals and to connect those signals to any callback function, either global or a member function, regardless of whether it is static or virtual. libsigsegv: libsigsegv/2.11-GCC-6.2.0, libsigsegv/2.11-GCCcore-6.4.0, ... GNU libsigsegv is a library for handling page faults in user mode. libsndfile: libsndfile/1.0.28-intel-2017.u2, ... Libsndfile is a C library for reading and writing files containing sampled sound (such as MS Windows WAV and the Apple/SGI AIFF format) through one standard library interface. libsodium: libsodium/1.0.17-intel-2016.u3 Sodium is a modern, easy-to-use software library for encryption, decryption, signatures, password hashing and more. libtool: libtool/2.4.5-GCC-4.9.2, libtool/2.4.6-GCC-4.6.4, ... GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries behind a consistent, portable interface. libunwind: libunwind/1.1-goolf-2015a The primary goal of libunwind is to define a portable and efficient C programming interface (API) to determine the call-chain of a program. The API additionally provides the means to manipulate the preserved (callee-saved) state of each call-frame and to resume execution at any point in the call-chain (non-local goto). The API supports both local (same-process) and remote (across-process) operation. As such, the API is useful in a number of applications libvorbis: libvorbis/1.3.5-GCC-6.2.0, libvorbis/1.3.5-intel-2016.u3, ... libwnck: libwnck/2.26.2-intel-2016.u3, libwnck/2.30.7-intel-2016.u3 - Homepage: https://download.gnome.org/sources/libwnck/ libxc: libxc/3.0.0-intel-2016.u3 Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals. - Homepage: http://www.tddft.org/programs/octopus/wiki/index.php/Libxc libxcb: libxcb/1.11-intel-2016.u3-Python-2.7.9, ... The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility. - Homepage: http://xcb.freedesktop.org/ libxfce4ui: libxfce4ui/4.12.0-intel-2016.u3, ... - Homepage: https://xfce.org/ libxfce4util: libxfce4util/4.12.1-intel-2016.u3 libxfce4util is part of xfce4 desktop - Homepage: http://xfce.org/ libxkbcommon: libxkbcommon/0.5.0-intel-2016.u3-Python-2.7.11, ... xkbcommon is a library to handle keyboard descriptions, including loading them from disk, parsing them and handling their state. It's mainly meant for client toolkits, window systems, and other system applications. - Homepage: http://xkbcommon.org/ libxml2: libxml2/2.7.8-GCC-4.9.2, libxml2/2.9.2-foss-2017b, ... Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable outside of the Gnome platform). - Homepage: http://xmlsoft.org/ libxslt: libxslt/1.1.26-GCC-4.9.2, libxslt/1.1.28-GCC-4.9.2, ... Libxslt is the XSLT C library developed for the GNOME project (but usable outside of the Gnome platform). - Homepage: http://xmlsoft.org/ libyaml: libyaml/0.1.6-intel-2016.u3, libyaml/0.1.7-intel-2017.u2, ... LibYAML is a YAML 1.1 parser and emitter written in C. - Homepage: http://pyyaml.org/wiki/LibYAML libzip: libzip/1.1.2-GCC-6.2.0, libzip/1.1.2-intel-2016.u3 libzip is a C library for reading, creating, and modifying zip archives.. - Homepage: https://nih.at/libzip/ likwid: likwid/4.2.0-foss-2017b, likwid/4.2.0-intel-2016.u3, ... Likwid stands for 'Like I knew what I am doing'. Likwid is a simple to install and use toolsuite of command line applications for performance oriented programmers. It works for Intel and AMD processors on the Linux operating system. llvmlite: llvmlite/0.22.0-intel-2017.u2-Python-3.6.4 A lightweight LLVM python binding for writing JIT compilers lmod: lmod Lmod: An Environment Module System lmoments3: lmoments3/1.0.4-intel-2017.u2-Python-3.6.4 rpy2 is Python 3.x library to estimate linear moments for statistical distribution functions. lobSTR: lobSTR/3.0.3-intel-2016.u3 lpsolve: lpsolve/5.5.2.5-intel-2016.u3, lpsolve/5.5.2.5-intel-2017.u2 Mixed Integer Linear Programming (MILP) solver lsd: lsd/0.3-GCC-4.9.2 LSD: LEAST-SQUARES METHODS TO ESTIMATE RATES AND DATES FROM SERIAL PHYLOGENIES lua: lua/5.3.1-GCC-4.9.2 lxde-icon-theme: lxde-icon-theme/0.5.1-intel-2016.u3 The LXDE Icon Theme package contains nuoveXT 2.2 Icon Theme for LXDE. - Homepage: http://lxde.org/ lxml: lxml/3.6.0-intel-2016.u3-Python-2.7.9, ... The lxml XML toolkit is a Pythonic binding for the C libraries libxml2 and libxslt. lynx: lynx/2.8.7-goolf-2015a lynx is an alphanumeric display oriented World-Wide Web Client - Homepage: http://lynx.isc.org/ lz4: lz4/1.8.2-goolf-2015a LZ4 is lossless compression algorithm, providing compression speed at 400 MB/s per core. It features an extremely fast decoder, with speed in multiple GB/s per core. lzma: lzma/4.32.7-foss-2017b, lzma/4.32.7-intel-2016.u3 LZMA Utils are based on LZMA SDK 4.32. LZMA Utils. magma: magma/2.2.0-intel-2017.u2-GCC-5.4.0-CUDA8 The MAGMA project aims to develop a dense linear algebra library similar to LAPACK but for heterogeneous/hybrid architectures, starting with current Multicore+GPU systems. make: make/4.1-GCC-4.9.2, make/4.1-GCC-6.2.0, make/4.1-gompi-2017.u1 GNU version of make utility - Homepage: http://www.gnu.org/software/make/make.html makedepend: makedepend/1.0.4-goolf-2015a, makedepend/1.0.5-GCC-4.9.2, ... The makedepend package contains a C-preprocessor like utility to determine build-time dependencies. - Homepage: http://www.linuxfromscratch.org/blfs/view/svn/x/makedepend.html matplotlib: matplotlib/1.5.1-intel-2016.u3-Python-2.7.9, ... matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python and ipython shell, web application servers, and six graphical user interface toolkits. - Homepage: http://matplotlib.org mccortex: mccortex/0.0.3 McCortex is a genome assembler and variant caller. It has a rich set of features for representing and manipulating genomes as graphs. md5deep: md5deep/4.4-intel-2016.u3 - Homepage: https://github.com/jessek/hashdeep/releases/tag/release-4.4 mercury: mercury/14.01.1-GCC-4.9.2, mercury/14.01.1-intel-2016.u3 Mercury is a pure logic programming language intended for the creation of large, fast, reliable programs. - Homepage: https://www.mercurylang.org/ mindboggle: mindboggle/1.2.4-intel-2017.u2-Python-3.6.1 Mindboggle’s open source brain morphometry platform takes in preprocessed T1-weighted MRI data, and outputs volume, surface, and tabular data containing label, feature, and shape information for further analysis. minimap2: minimap2/2.11-intel-2017.u2 Minimap2 is a fast sequence mapping and alignment program that can find overlaps between long noisy reads, or map long reads or their assemblies to a reference genome optionally with detailed alignment (i.e. CIGAR). At present, it works efficiently with query sequences from a few kilobases to ~100 megabases in length at an error rate ~15%. Minimap2 outputs in the PAF or the SAM format. On limited test data sets, minimap2 is over 20 times faster than most other long-read aligners. It will replace BWA-MEM for long reads and contig alignment. mkl-dnn: mkl-dnn/0.13-intel-2018.u4 Intel(R) Math Kernel Library for Deep Neural Networks (Intel(R) MKL-DNN) mlst: mlst/2.16-spartan_intel-2017.u2 Scan contig files against traditional PubMLST typing schemes. molcas: molcas/8.2.170401-OpenMPI-2.0.2-intel-2016.u3-imkl-11.3.3.210, ... Molcas is an ab initio quantum chemistry software package developed by scientists to be used by scientists. The basic philosophy is is to be able to treat general electronic structures for molecules consisting of atoms from most of the periodic table. As such, the primary focus of the package is on multiconfigurational methods with applications typically connected to the treatment of highly degenerate states. Key aspects of Molcas: SCF/DFT, CASSCF/RASSCF, CASPT2/RASPT2 Fast, accurate, and robust code Free support and updates Molcas is not a black box tool. The user should be an educated quantum chemist, with some knowledge about the different quantum chemical models in use today, their application areas and their inherent accuracy. The MOLCAS group arranges regular MOLCAS workshops, which teaches how to use the software. motif: motif/2.3.5-goolf-2015a, motif/2.3.5-intel-2016.u3 Motif refers to both a graphical user interface (GUI) specification and the widget toolkit for building applications that follow that specification under the X Window System on Unix and other POSIX-compliant systems. It was the standard toolkit for the Common Desktop Environment and thus for Unix. - Homepage: http://motif.ics.com/ mpj: mpj/0.44 mpmath: mpmath/0.19-intel-2016.u3-Python-2.7.11 mpmath can be used as an arbitrary-precision substitute for Python's float/complex types and math/cmath modules, but also does much more advanced mathematics. Almost any calculation can be performed just as well at 10-digit or 1000-digit precision, with either real or complex numbers, and in many cases mpmath implements efficient algorithms that scale well for extremely high precision work. - Homepage: http://mpmath.org/ ms: ms/08112017-GCC-4.9.3 The purpose of this program is to allow one to investigate the statistical properties of such samples, to evaluate estimators or statistical tests, and generally to aid in the interpretation of polymorphism data sets. msms: msms/3.2rc-b163-Java-1.8.0_71 MSMS is a coalescent simulator that models itself off Hudsons ms in usage and includes selection. It is fast, often faster than ms, and portable running on Mac OSX, windows and Linux. By using this tool, one can study the patterns of selection in complicated demographic scenarios. mykrobe: mykrobe/0.3.6-Python-2.7.10-bundle The Mykrobe predictor is designed for use by microbiologists and doctors, providing information needed in order to choose the best treatment. It analyses the whole genome of a bacterial sample, all within a couple of minutes, and predicts which drugs the infection is resistant to. nanopolish: nanopolish/0.9.2-intel-2017.u2 Software package for signal-level analysis of Oxford Nanopore sequencing data. ncbi-vdb: ncbi-vdb/2.9.3-spartan_intel-2017.u2 The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives. ncurses: ncurses/5.9-GCC-4.6.4, ncurses/5.9-GCC-4.9.2, ... The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses. - Homepage: http://www.gnu.org/software/ncurses/ ncview: ncview/2.1.7-intel-2016.u3 Ncview is a visual browser for netCDF format files. Typically you would use ncview to get a quick and easy, push-button look at your netCDF files. You can view simple movies of the data, view along various dimensions, take a look at the actual data values, change color maps, invert the data, etc. - Homepage: http://meteora.ucsd.edu/~pierce/ncview_home_page.html netCDF: netCDF/4.3.2-GCC-4.9.2, netCDF/4.3.2-intel-2016.u3, ... NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. - Homepage: http://www.unidata.ucar.edu/software/netcdf/ netCDF-Fortran: netCDF-Fortran/4.4.0-GCC-4.9.2, ... NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. netcdf4-python: ... Python/numpy interface to netCDF. nettle: nettle/3.2-GCC-4.9.2, nettle/3.2-GCC-6.2.0, ... Nettle is a cryptographic library that is designed to fit easily in more or less any context: In crypto toolkits for object-oriented languages (C++, Python, Pike, ...), in applications like LSH or GNUPG, or even in kernel space. - Homepage: http://www.lysator.liu.se/~nisse/nettle/ networkx: networkx/2.2-intel-2017.u2-Python-3.6.4 NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks. ns: ns/3.27-GCC-4.9.2 Ns-3 is a discrete event simulator targeted at networking research. nullarbor: nullarbor/2.0.20181010-spartan_gcc-6.2.0, ... Pipeline to generate complete public health microbiology reports from sequenced isolates. numactl: numactl/2.0.10-GCC-4.6.4, numactl/2.0.10-GCC-4.9.2, ... numba: numba/0.36.2-intel-2017.u2-Python-3.6.4 numexpr: numexpr/2.6.4-intel-2017.u2-Python-3.6.4 The numexpr package evaluates multiple-operator array expressions many times faster than NumPy can. It accepts the expression as a string, analyzes it, rewrites it more efficiently, and compiles it on the fly into code for its internal virtual machine (VM). Due to its integrated just-in-time (JIT) compiler, it does not require a compiler at runtime. numpy: numpy/1.8.2-intel-2016.u3-Python-2.7.9, ... NumPy is the fundamental package for scientific computing with Python. It contains among other things: a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases. nvptx-tools: nvptx-tools/1.0-GCCcore-8.2.0 nvptx-tools: a collection of tools for use with nvptx-none GCC toolchains. orfm: orfm/0.7.1 A simple and not slow open reading frame (ORF) caller. No bells or whistles like frameshift detection, just a straightforward goal of returning a FASTA file of open reading frames over a certain length from a FASTA/Q file of nucleotide sequences. pandas: pandas/0.18.1-intel-2016.u3-Python-3.5.2, ... Powerful data structures for data analysis, time series,and statistics pandoc: pandoc/2.0.3 Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. parallel: parallel/20141122-GCC-4.9.2, parallel/20141122-intel-2016.u3, ... parsnp: parsnp/1.2 Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. patchelf: patchelf/0.8-GNU-4.9.2-2.25 PatchELF is a small utility to modify the dynamic linker and RPATH of ELF executables. - Homepage: http://nixos.org/patchelf.html petsc4py: petsc4py/3.6.0-intel-2016.u3-Python-2.7.9, ... petsc4py are Python bindings for PETSc, the Portable, Extensible Toolchain for Scientific Computation. - Homepage: https://bitbucket.org/petsc/petsc4py picard: picard/1.127, picard/2.3.0, picard/2.6.0, picard/2.18.27 A set of tools (in Java) for working with next generation sequencing data in the BAM format. pilon: pilon/1.21-Java-1.8.0_71 Pilon is a software tool which can be used to: Automatically improve draft assemblies Find variation among strains, including large event detection pinfish: pinfish/20181106 Pinfish is a collection of tools helping to make sense of long transcriptomics data (long cDNA reads, direct RNA reads). pixman: pixman/0.32.6-foss-2017b, pixman/0.32.6-GCC-4.9.2, ... pkg-config: pkg-config/0.29-GCC-4.9.2, pkg-config/0.29-goolf-2015a, ... pkg-config is a helper tool used when compiling applications and libraries. It helps you insert the correct compiler options on the command line so an application can use gcc -o test test.c `pkg-config --libs --cflags glib-2.0` for instance, rather than hard-coding values on where to find glib (or other libraries). - Homepage: http://www.freedesktop.org/wiki/Software/pkg-config/ plotly: plotly/1.12.2-intel-2016.u3-Python-3.5.2, ... Python plotting library for collaborative, interactive, publication-quality graphs. plumed: plumed/2.2.3-intel-2016.u3 PLUMED is an open source library for free energy calculations in molecular systems which works together with some of the most popular molecular dynamics engines. Free energy calculations can be performed as a function of many order parameters with a particular focus on biological problems, using state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. pplacer: pplacer/1.1 Pplacer places query sequences on a fixed reference phylogenetic tree to maximize phylogenetic likelihood or posterior probability according to a reference alignment. printproto: printproto/1.0.5-intel-2016.u3, ... X.org PrintProto protocol headers. - Homepage: http://xorg.freedesktop.org/ prokka: prokka/1.13-spartan_gcc-6.2.0, prokka/1.13-spartan_intel-2017.u2 Prokka is a software tool for the rapid annotation of prokaryotic genomes. protobuf: protobuf/2.6.1-GCC-4.9.2, protobuf/2.6.1-GCC-6.2.0, ... protobuf-python: protobuf-python/3.3.0-intel-2016.u3-Python-3.5.2, ... Python Protocol Buffers runtime library. - Homepage: https://github.com/google/protobuf/ psycopg2: psycopg2/2.7.5-goolf-2015a-Python-2.7.12 Psycopg is the most popular PostgreSQL adapter for the Python programming language. At its core it fully implements the Python DB API 2.0 specifications. pyMESS: pyMESS/0.32.1-spartan_intel-2017.u2-Python-2.7.13 pyMESS is python package for MESS pybedtools: pybedtools/0.7.10-intel-2017.u2-Python-3.6.4 Wrapper around BEDTools for bioinformatics work pychopper: pychopper/0.2.0-intel-2017.u2-Python-3.5.2 A tool to identify full length cDNA reads. pydicom: pydicom/0.9.9-intel-2016.u3-Python-2.7.9 Read, modify and write DICOM files with python code - Homepage: https://github.com/darcymason/pydicom pyseer: pyseer/1.1.2-intel-2017.u2-Python-3.6.4 SEER, reimplemented in python pyshp: pyshp/1.2.12-goolf-2015a-Python-2.7.12 The dateutil module provides powerful extensions to the datetime module available in the Python standard library. - Homepage: https://pypi.python.org/pypi/python-dateutil pysqlite: pysqlite/2.6.3-intel-2016.u3-Python-2.7.9 pysqlite is an interface to the SQLite 3.x embedded relational database engine. It is almost fully compliant with the Python database API version 2.0 also exposes the unique features of SQLite. - Homepage: https://pypi.python.org/pypi/pysqlite python-dateutil: python-dateutil/2.6.1-goolf-2015a-Python-2.7.12 The dateutil module provides powerful extensions to the datetime module available in the Python standard library. - Homepage: https://pypi.python.org/pypi/python-dateutil rainbow: rainbow/2.0.4-foss-2017b Efficient tool for clustering and assembling short reads, especially for RAD. randrproto: randrproto/1.5.0-intel-2016.u3, ... Xrandr protocol and ancillary headers - Homepage: http://www.freedesktop.org/wiki/Software/xlibs recentrifuge: recentrifuge/20181019-intel-2017.u2 Robust comparative analysis and contamination removal for metagenomics redis: redis/5.0.3-GCC-6.2.0 Redis is an open source (BSD licensed), in-memory data structure store, used as a database, cache and message broker. renderproto: renderproto/0.11-intel-2016.u3, ... Xrender protocol and ancillary headers - Homepage: http://www.freedesktop.org/wiki/Software/xlibs requests: requests/2.7.0-intel-2016.u3-Python-2.7.9, ... Python http for humans rpy2: rpy2/2.9.4-intel-2017.u2-Python-3.6.4 rpy2 is a redesign and rewrite of rpy. It is providing a low-level interface to R from Python, a proposed high-level interface, including wrappers to graphical libraries, as well as R-like structures and functions. ruffus: ruffus/2.6.3-intel-2016.u3-Python-2.7.10 The Ruffus module is a lightweight way to add support for running computational pipelines. scikit-learn: scikit-learn/0.18-intel-2016.u3-Python-2.7.9, ... Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, building upon numpy, scipy, and matplotlib. As a machine-learning module, it provides versatile tools for data mining and analysis in any field of science and engineering. It strives to be simple and efficient, accessible to everybody, and reusable in various contexts. - Homepage: http://scikit-learn.org/stable/index.html scrm: scrm/1.7.2-GCC-4.9.2 scrm simulates the evolution of genetic sequences. It takes a neutral evolutionary model as input, and generates random sequences that evolved under the model. As coalescent simulator, it traces the ancestry of the sampled sequences backwards in time and is therefore extremely efficient. Compared to other coalescent simulators, it can simulate chromosome-scale sequences without a measureable reduction of genetic linkage between different sites. sdsl-lite: sdsl-lite/2.0.3-spartan_intel-2017.u2 The Succinct Data Structure Library (SDSL) is a powerful and flexible C++11 library implementing succinct data structures. In total, the library contains the highlights of 40 research publications. seqtk: seqtk/1.2-r94-intel-2016.u3 Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. settarg: settarg sharedmem: sharedmem/0.3.5-intel-2017.u2-Python-3.6.4 A different flavor of multiprocessing in Python showq: showq/0.12, showq/0.15 slepc4py: slepc4py/3.6.0-intel-2016.u3-Python-2.7.9, ... Python bindings for SLEPc, the Scalable Library for Eigenvalue Problem Computations. - Homepage: https://bitbucket.org/slepc/slepc4py slurm: slurm/latest slurm_drmaa: slurm_drmaa/1.0.7-GCC-4.9.2 smafa: smafa/0.1.2 Smafa attempts to align or cluster pre-aligned biological sequences, handling sequences which are all the same length. smart-open: smart-open/1.8.0-intel-2016.u3-Python-2.7.12, ... Scalable statistical semantics, Analyze plain-text documents for semantic structure, Retrieve semantically similar documents snakemake: snakemake/5.3.0-intel-2017.u2-Python-3.6.4 The Snakemake workflow management system is a tool to create reproducible and scalable data analyses. snappy: snappy/1.1.6-intel-2017.u2-GCC-5.4.0-CUDA8, snappy/1.1.6 Snappy is a compression/decompression library. It does not aim for maximum compression, or compatibility with any other compression library; instead, it aims for very high speeds and reasonable compression. snpEff: snpEff/4.1d-Java-1.7.0_80, snpEff/4.2-Java-1.8.0_71, ... SnpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of genetic variants (such as amino acid changes). sparsehash: sparsehash/2.0.2-goolf-2015a, sparsehash/2.0.3-intel-2016.u3 An extremely memory-efficient hash_map implementation. 2 bits/entry overhead! The SparseHash library contains several hash-map implementations, including implementations that optimize for space or speed. spartan: spartan/2016-03 spartan-gpgpu: spartan-gpgpu/2018.u4 Intel Cluster Toolchain Compiler Edition Intel C/C++ and Fortran compilers, Intel MKL, plus nVidia CUDA. With added OpenMPI using ucx, tuned for Spartan's gpgpu cluster. spartan_gcc: spartan_gcc/6.2.0-cuda9.2, spartan_gcc/6.2.0, ... Spartan GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK. spartan_gompi: spartan_gompi/GCC-6.2.0-OpenMPI-3.0.0, ... GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support. spartan_intel: spartan_intel/2017.u2-cuda9.1, spartan_intel/2017.u2 Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & OpenMPI. startup-notification: startup-notification/0.12-intel-2016.u3 startup-notification contains a reference implementation of the startup notification protocol. The reference implementation is mostly under an X Window System style license, and has no special dependencies. - Homepage: http://www.freedesktop.org/wiki/Software/startup-notification statsmodels: statsmodels/0.9.0-intel-2017.u2-Python-3.6.4 statsmodels is a Python module that provides classes and functions for the estimation of many different statistical models, as well as for conducting statistical tests, and statistical data exploration. supernova: supernova/2.1.1 Supernova is a software package for de novo assembly from Chromium Linked-Reads that are made from a single whole-genome library from an individual DNA source sympy: sympy/0.7.6-goolf-2015a-Python-2.7.10, ... SymPy is a Python library for symbolic mathematics. It aims to become a full-featured computer algebra system (CAS) while keeping the code as simple as possible in order to be comprehensible and easily extensible. SymPy is written entirely in Python and does not require any external libraries. tabix: tabix/0.2.6-foss-2017b, tabix/0.2.6-GCCcore-6.4.0, ... Generic indexer for TAB-delimited genome position files taxator-tk: taxator-tk/1.3.3-intel-2016.u3-Python-2.7.11 A set of programs for the taxonomic analysis of nucleotide sequence data . tbl2asn: tbl2asn/24.3, tbl2asn/24.9, tbl2asn/25.0 tcsh: tcsh/6.18.01-intel-2016.u3, tcsh/6.20.00-intel-2017.u2, ... Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). It is a command language interpreter usable both as an interactive login shell and a shell script command processor. It includes a command-line editor, programmable word completion, spelling correction, a history mechanism, job control and a C-like syntax. - Homepage: http://www.tcsh.org texinfo: texinfo/6.5-GCC-6.2.0 Texinfo is the official documentation format of the GNU project. texlive: texlive/2017-GCC-4.9.2, texlive/2017-GCC-6.2.0 TeX Live is an easy way to get up and running with the TeX document production system. It provides a comprehensive TeX system with binaries for most flavors of Unix, including GNU/Linux, and also Windows. It includes all the major TeX-related programs, macro packages, and fonts that are free software, including support for many languages around the world. trimAI: trimAI/1.4.1-spartan_gcc-6.2.0 Multiple sequence alignments (MSA) are central to many areas of bioinformatics and evolutionary biology. tumbler: tumbler/0.1.31-intel-2016.u3 - Homepage: http:/xfce.org/ unicycler: unicycler/0.4.7-GCC-6.2.0-Python-3.5.2 Unicycler is a hybrid assembly pipeline for bacterial genomes. It uses both Illumina reads and long reads (PacBio or Nanopore) to produce complete and accurate assemblies unimelb-mf-clients: unimelb-mf-clients/current unixODBC: unixODBC/2.3.4-GCC-4.9.2 urllib3: urllib3/1.24.1-GCC-6.2.0 HTTP library with thread-safe connection pooling, file post, and more util-linux: util-linux/2.26.1-intel-2016.u3, util-linux/2.28-goolf-2015a, ... Set of Linux utilities - Homepage: http://www.kernel.org/pub/linux/utils/util-linux vcfanno: vcfanno/0.3.1 vcfanno allows you to quickly annotate your VCF with any number of INFO fields from any number of VCFs or BED files. vsearch: vsearch/2.0.3-goolf-2015a, vsearch/2.0.3-intel-2016.u3, ... The aim of this project is to create an alternative to the USEARCH tool developed by Robert C. Edgar (2010). vtk_cpp_tools: vtk_cpp_tools/7.1.1-intel-2017.u2 web_proxy: web_proxy/latest wget: wget/1.19.4-GCC-8.2.0, wget/1.19.4-intel-2016.u3, ... GNU Wget is a free software package for retrieving files using HTTP, HTTPS and FTP, the most widely-used Internet protocols. It is a non-interactive commandline tool, so it may easily be called from scripts, cron jobs, terminals without X-Windows support, etc. wheel: wheel/0.32.1-spartan_intel-2017.u2-Python-2.7.13, ... This library is the reference implementation of the Python wheel packaging standard, as defined in PEP 427. wxPython: wxPython/3.0.2.0-intel-2017.u2-Python-2.7.13 wxPython is a GUI toolkit for the Python programming language. It allows Python programmers to create programs with a robust, highly functional graphical user interface, simply and easily. It is implemented as a Python extension module (native code) that wraps the popular wxWidgets cross platform GUI library, which is written in C++. wxWidgets: wxWidgets/3.0.2-intel-2017.u2, wxWidgets/3.1.0-GCC-4.9.2, ... wxWidgets is a C++ library that lets developers create GUI applications. x264: x264/20160614-GCC-4.9.2, x264/20160614-intel-2016.u3, ... x264 is a free software library and application for encoding video streams into the H.264/MPEG-4 AVC compression format, and is released under the terms of the GNU GPL. x265: x265/2.9-spartan_gcc-6.2.0, x265/2.9-spartan_intel-2017.u2 x265 is a free software library and application for encoding video streams into the H.265 AVC compression format, and is released under the terms of the GNU GPL. xbitmaps: xbitmaps/1.1.1-goolf-2015a, xbitmaps/1.1.1-intel-2016.u3 provides bitmaps for x - Homepage: http://www.freedesktop.org/wiki/Software/xlibs xcb-proto: xcb-proto/1.11-GCC-4.9.2-Python-2.7.9, ... The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility. xcb-util: xcb-util/0.4.0-intel-2016.u3-Python-2.7.11, ... The xcb-util package provides additional extensions to the XCB library, many that were previously found in Xlib, but are not part of core X protocol - Homepage: http://xcb.freedesktop.org/ xcb-util-image: xcb-util-image/0.4.0-intel-2016.u3-Python-2.7.11, ... The xcb-util-image package provides additional extensions to the XCB library. - Homepage: http://xcb.freedesktop.org/ xcb-util-keysyms: xcb-util-keysyms/0.4.0-intel-2016.u3, ... The xcb-util-keysyms package contains a library for handling standard X key constants and conversion to/from keycodes. - Homepage: http://xcb.freedesktop.org/ xcb-util-renderutil: ... The xcb-util-renderutil package provides additional extensions to the XCB library. - Homepage: http://xcb.freedesktop.org/ xcb-util-wm: xcb-util-wm/0.4.1-intel-2016.u3-Python-2.7.11, ... The xcb-util-wm package contains libraries which provide client and window-manager helpers for EWMH and ICCCM. - Homepage: http://xcb.freedesktop.org/ xextproto: xextproto/7.3.0-GCC-4.9.2, xextproto/7.3.0-GCC-6.2.0, ... XExtProto protocol headers. - Homepage: http://www.freedesktop.org/wiki/Software/xlibs xf86vidmodeproto: xf86vidmodeproto/2.3.1-GCC-6.2.0 X11 XFree86 video mode extension protocol headers. xfce4: xfce4/4.12-intel-2016.u3 xfce4-appfinder: xfce4-appfinder/4.12.0-intel-2016.u3 - Homepage: http:/xfce.org/ xfce4-panel: xfce4-panel/4.12.0-intel-2016.u3 - Homepage: http:/xfce.org/ xfce4-session: xfce4-session/4.12.1-intel-2016.u3 - Homepage: http://xfce.org xfce4-settings: xfce4-settings/4.12.1-intel-2016.u3 - Homepage: http://xfce.com xfconf: xfconf/4.12.0-intel-2016.u3 - Homepage: https://xfce.org/ xfdesktop: xfdesktop/4.12.0-intel-2016.u3 xfce4 Desktop - Homepage: http://xfce.org xfwm4: xfwm4/4.12.0-intel-2016.u3 xfce4 Window Manager - Homepage: http://xfce.org xineramaproto: xineramaproto/1.2.1-intel-2016.u3, ... X protocol and ancillary headers for xinerama - Homepage: http://www.freedesktop.org/wiki/Software/xlibs xorg-macros: xorg-macros/1.17-GCC-4.9.2, xorg-macros/1.17-GCC-6.2.0, ... xplor-nih: xplor-nih/2.47 XPLOR-NIH is a structure determination program which builds on the X-PLOR program, including additional tools developed at the NIH. xprop: xprop/1.2.2-intel-2016.u3, xprop/1.2.2-intel-2017.u2 The xprop utility is for displaying window and font properties in an X server. One window or font is selected using the command line arguments or possibly in the case of a window, by clicking on the desired window. A list of properties is then given, possibly with formatting information. - Homepage: http://www.x.org/wiki/ xproto: xproto/7.0.27-GCC-4.9.2, xproto/7.0.27-intel-2016.u3, ... X protocol and ancillary headers - Homepage: http://www.freedesktop.org/wiki/Software/xlibs xtrans: xtrans/1.3.5-GCC-4.9.2, xtrans/1.3.5-GCC-6.2.0, ... xtrans includes a number of routines to make X implementations transport-independent; at time of writing, it includes support for UNIX sockets, IPv4, IPv6, and DECnet. - Homepage: http://www.freedesktop.org/wiki/Software/xlibs zlib: zlib/1.2.7-intel-2016.u3, zlib/1.2.8-foss-2017b, ... zlib is designed to be a free, general-purpose, legally unencumbered -- that is, not covered by any patents -- lossless data-compression library for use on virtually any computer hardware and operating system. zsh: zsh/5.2 Zsh is a shell designed for interactive use, although it is also a powerful scripting language. zstd: zstd/1.3.4-goolf-2015a Zstandard is a real-time compression algorithm, providing high compression ratios. It offers a very wide range of compression/speed trade-off, while being backed by a very fast decoder. It also offers a special mode for small data, called dictionary compression, and can create dictionaries from any sample set. zsync: zsync/0.6.2-goolf-2015a zsync-0.6.2: Optimising file distribution program, a 1-to-many rsync ---------------------------------------------------------------------------- To learn more about a package execute: $ module spider Foo where "Foo" is the name of a module. To find detailed information about a particular package you must specify the version if there is more than one version: $ module spider Foo/11.1 ----------------------------------------------------------------------------