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Summary

The 2022.1 Argon Software Stack is quite a bit different on the backend from previous stacks. This leads to some differences in behavior when interacting with the stack and this will be discussed below. The goal is that using this stack should be familiar but hopefully a little better as well. Many packages have been updated and new packages have been added and more will be added over time. As always, please report any issues to research-computing@uiowa.edu.

What is new

Distribution Mechanism

Up until now all of the software stacks have been distributed to login and compute nodes via NFS (Network File System). Beginning with the 2022.1 stack the distribution mechanism will use the CernVM File System, also known as CVMFS. This is designed for software distribution over a wide network and it is felt that this will be an improvement in how software is delivered to the Argon login and compute nodes. Note that this does not apply to the older software stacks which will continue to be deployed via NFS. In addition, for technical reasons, the environment module files and links to binaries are still served via NFS. Finally, licensed software on Argon will continue to be distributed via NFS. This is to avoid violating license terms when the Argon stack is eventually made available to run on systems other than Argon.

Gentoo Prefix Middle Layer

A Gentoo Prefix layer is put on top of the OS layer and the software packages are linked to the libraries of this middle layer. This layer is exported via CVMFS along with the software packages. The goal of this is to make the packages as independent of the underlying OS as possible. The primary motivation for this is to make it possible to upgrade or change the underlying OS without breaking the ability of the software to run on the newer OS. This also lays the foundation for being able to run the Argon software stack on non-Argon systems, but that is further down the road. Finally, this can also play a role in software reproducibility. This is effectively a cross-compiled environment and there are some caveats that come with that, which will be discussed below. Note that there could be some issues due to using a middle layer, so please report if something seems odd or broken.

Native Lua module files for LMod

Argon uses Lmod for environment modules but previous software stacks used TCL based environment module files for historical and technical reasons. Those TCL files needed to be converted to Lua files on the fly, and while that is a pretty fast conversion it does add overhead. The Lmod Lua files should provide a performance boost for searching for and loading modules and also provides extra capabilities.

What this all means

Running software packages

In prior stacks the only purpose of the "stack" environment module was to manipulate the module path such that the respective packages of that stack were made available to load. With the middle layer, loading the "stack/2022.1" module will not only manipulate the module path but it will effectively load a new Linux environment. This will replace many of the OS commands. One of the issues that has been present is that loading an environment module can alter the environment such that system commands break. Good examples of that were editors like vim and emacs. That was alleviated by providing packages for vim and emacs to replace the system ones. The concept is the same here except that now the replacements will be in the stack module itself, with no need to load additional modules. In addition to many common system commands, below is a list of some important packages that are loaded in the environment by the stack/2022.1 module:

  • GCC
  • autotools utilities
  • cmake
  • gmake
  • tar
  • meson
  • git
  • ninja
  • texinfo
  • perl
  • python
  • rust
  • emacs
  • vim

The caveat here is that since many commands are replaced, with newer versions than the system commands, there could be differences in behavior when switching between using the 2022.1 stack and other stacks.

Another change in behavior is with regard to environment module dependencies. Since the 2022.1 stack uses Lmod native Lua files now, module dependencies are handled in a more intelligent way. As always, when loading a module, modules for dependencies are also loaded. What is different now is the unloading behavior. Previously, unloading a module would only unload the specified module, leaving the rest of the stack in place, which is probably more modules than desired. With the 2022.1 stack, unloading a module will also unload the dependencies that were previously loaded. In addition, if an underlying dependency is unloaded a message will be printed so at least you know about the now missing dependency. Here is an example to illustrate.

module load stack/2022.1
module list

Currently Loaded Modules:
  1) stack/2022.1

Load a module with dependencies

module load py-tensorflow-estimator
module list

Currently Loaded Modules:
  1) stack/2022.1                         27) py-wheel/0.37.0_gcc-9.4.0               53) py-cffi/1.15.0_gcc-9.4.0
  2) cuda/11.4.4_gcc-9.4.0                28) py-astunparse/1.6.3_gcc-9.4.0           54) py-semantic-version/2.8.2_gcc-9.4.0
  3) cudnn/8.2.4.15-11.4_gcc-9.4.0        29) py-gast/0.4.0_gcc-9.4.0                 55) py-toml/0.10.2_gcc-9.4.0
  4) python/3.9.9_gcc-9.4.0               30) py-google-pasta/0.2.0_gcc-9.4.0         56) rust/1.58.1_gcc-9.4.0
  5) flatbuffers/1.12.0_gcc-9.4.0         31) c-ares/1.15.0_gcc-9.4.0                 57) py-setuptools-rust/0.12.1_gcc-9.4.0
  6) intel-oneapi-mkl/2022.0.2_gcc-9.4.0  32) re2/2021-06-01_gcc-9.4.0                58) py-cryptography/36.0.1_gcc-9.4.0
  7) rdma-core/39.0_gcc-9.4.0             33) py-grpcio/1.43.0_gcc-9.4.0              59) py-pyjwt/2.1.0_gcc-9.4.0
  8) nccl/2.11.4-1_gcc-9.4.0              34) libaec/1.0.5_gcc-9.4.0                  60) py-oauthlib/3.1.0_gcc-9.4.0
  9) libpciaccess/0.16_gcc-9.4.0          35) pkgconf/1.8.0_gcc-9.4.0                 61) py-certifi/2021.10.8_gcc-9.4.0
 10) libiconv/1.16_gcc-9.4.0              36) hdf5/1.12.1_gcc-9.4.0-mpi               62) py-charset-normalizer/2.0.12_gcc-9.4.0
 11) xz/5.2.5_gcc-9.4.0                   37) py-mpi4py/3.1.2_gcc-9.4.0               63) py-idna/3.3_gcc-9.4.0
 12) zlib/1.2.11_gcc-9.4.0                38) py-setuptools/59.4.0_gcc-9.4.0          64) py-urllib3/1.26.6_gcc-9.4.0
 13) libxml2/2.9.12_gcc-9.4.0             39) py-numpy/1.21.5_gcc-9.4.0               65) py-requests/2.26.0_gcc-9.4.0
 14) ncurses/6.2_gcc-9.4.0                40) py-h5py/3.6.0_gcc-9.4.0-mpi             66) py-requests-oauthlib/1.3.0_gcc-9.4.0
 15) hwloc/2.7.0_gcc-9.4.0                41) py-keras-preprocessing/1.1.2_gcc-9.4.0  67) py-google-auth-oauthlib/0.4.6_gcc-9.4.0
 16) openssl/1.1.1m_gcc-9.4.0             42) py-libclang/11.1.0_gcc-9.4.0            68) py-markdown/3.3.4_gcc-9.4.0
 17) libevent/2.1.12_gcc-9.4.0            43) py-opt-einsum/3.3.0_gcc-9.4.0           69) py-tensorboard-data-server/0.6.1_gcc-9.4.0
 18) numactl/2.0.14_gcc-9.4.0             44) py-protobuf/3.17.3_gcc-9.4.0            70) py-tensorboard-plugin-wit/1.8.1_gcc-9.4.0
 19) opa-psm2/11.2.206_gcc-9.4.0          45) py-cachetools/4.2.4_gcc-9.4.0           71) py-werkzeug/2.0.2_gcc-9.4.0
 20) ucx/1.10.1_gcc-9.4.0                 46) py-pyasn1/0.4.8_gcc-9.4.0               72) py-tensorboard/2.7.0_gcc-9.4.0
 21) libfabric/1.14.0_gcc-9.4.0           47) py-pyasn1-modules/0.2.8_gcc-9.4.0       73) py-termcolor/1.1.0_gcc-9.4.0
 22) openssh/8.8p1_gcc-9.4.0              48) py-rsa/4.7.2_gcc-9.4.0                  74) py-typing-extensions/3.10.0.2_gcc-9.4.0
 23) openmpi/4.1.2_gcc-9.4.0              49) py-google-auth/2.3.2_gcc-9.4.0          75) py-wrapt/1.13.3_gcc-9.4.0
 24) protobuf/3.17.3_gcc-9.4.0            50) py-blinker/1.4_gcc-9.4.0                76) py-tensorflow/2.7.0_gcc-9.4.0
 25) py-six/1.16.0_gcc-9.4.0              51) libffi/3.4.2_gcc-9.4.0                  77) py-keras/2.7.0_gcc-9.4.0
 26) py-absl-py/0.13.0_gcc-9.4.0          52) py-pycparser/2.20_gcc-9.4.0             78) py-tensorflow-estimator/2.7.0_gcc-9.4.0

Unload the same module.

module unload py-tensorflow-estimator 
module list

Currently Loaded Modules:
  1) stack/2022.1

Reload the module.

module load py-tensorflow-estimator

Unload a dependency.

module unload py-tensorflow
-------------------------------------------------------------------------------------------------------------------------------------------
The following dependent module(s) are not currently loaded: py-tensorflow/2.7.0_gcc-9.4.0 (required by: py-keras/2.7.0_gcc-9.4.0, py-tensorflow-estimator/2.7.0_gcc-9.4.0)
-------------------------------------------------------------------------------------------------------------------------------------------

CUDA GPU

Software that uses CUDA ultimately depends on a kernel module to access the hardware. The library interfaces to the kernel module must be part of the OS layer. In order to facilitate communication between the software packages and the kernel drivers, the libraries are linked in the middle layer. This is the same thing that is done with container images. What is important to note is that there can only be one driver at a time and it will likely change as OS updates happen. This is no different from the past stacks which would have a locked version of cuda, but would use whatever driver is installed in the OS. In other words, there is no Nvidia CUDA driver version that is part of the 2022.1 stack, or any stack, or any container. The only difference here is that there is now a set of links that are part of the stack, but what they point to is part of the OS. This may also become important if the Argon software stack is run on a non-Argon system.

MPI

Similar to CUDA, there are drivers at the OS layer that provide access to the high speed interconnect fabric. The abstracted fabric layers should be able to interface to the underlying drivers, but again, there is a dependency on the underlying OS, where things could change over time or vary across systems.

Development

While the primary purpose of the software stack is for running software the environment modules also provide variables needed for development. This may look a little different with the 2022.1 stack as it is a cross-compiled environment. It is possible that software developed using previous stacks will not run in this environment and would need to be recompiled. This would be due to the use of a different SYSROOT. If you are developing software that uses the 2022.1 stack you will need to make sure that you are not picking up any headers or libraries from the OS in your build system, ie., 

  • /lib
  • /lib64
  • /usr/lib
  • /usr/lib64
  • /usr/include

Instead, the above should be prefixed with ${EPREFIX}, which points to the SYSROOT used by the stack. In addition, use the gcc or oneapi compilers from this environment, which are already aware of the SYSROOT. Note that the NVHPC compiler is untested.

Software list

Package
(links to external page)

Versions Description

gurobi

9.5.1

The Gurobi Optimizer was designed from the ground up to be the fastest, most powerful solver available for your LP, QP, QCP, and MIP (MILP, MIQP, and MIQCP) problems.

hwloc

2.7.0

The Hardware Locality (hwloc) software project.

intel-oneapi-mkl

2022.0.2

Intel oneAPI MKL.

libevent

2.1.12

The libevent API provides a mechanism to execute a callback function when a specific event occurs on a file descriptor or after a timeout has been reached. Furthermore, libevent also support callbacks due to signals or regular timeouts.

libfabric

1.14.0

The Open Fabrics Interfaces (OFI) is a framework focused on exporting fabric communication services to applications.

libiconv

1.16

GNU libiconv provides an implementation of the iconv() function and the iconv program for character set conversion.

libpciaccess

0.16

Generic PCI access library.

libxml2

2.9.12

Libxml2 is the XML C parser and toolkit developed for the Gnome project (but usable outside of the Gnome platform), it is free software available under the MIT License.

lz4

1.9.3

LZ4 is lossless compression algorithm, providing compression speed at 400 MB/s per core, scalable with multi-cores CPU. It also features an extremely fast decoder, with speed in multiple GB/s per core, typically reaching RAM speed limits on multi-core systems.

matlab

R2021b

MATLAB (MATrix LABoratory) is a multi-paradigm numerical computing environment and fourth-generation programming language. A proprietary programming language developed by MathWorks, MATLAB allows matrix manipulations, plotting of functions and data, implementation of algorithms, creation of user interfaces, and interfacing with programs written in other languages, including C, C++, C#, Java, Fortran and Python.

ncurses

6.2

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.

netlib-scalapack

2.1.0

ScaLAPACK is a library of high-performance linear algebra routines for parallel distributed memory machines

numactl

2.0.14

NUMA support for Linux

opa-psm2

11.2.206

Omni-Path Performance Scaled Messaging 2 (PSM2) library

openmpi

4.1.2

An open source Message Passing Interface implementation.

openssh

8.8p1

OpenSSH is the premier connectivity tool for remote login with the SSH protocol. It encrypts all traffic to eliminate eavesdropping, connection hijacking, and other attacks. In addition, OpenSSH provides a large suite of secure tunneling capabilities, several authentication methods, and sophisticated configuration options.

openssl

1.1.1m

OpenSSL is an open source project that provides a robust, commercial-grade, and full-featured toolkit for the Transport Layer Security (TLS) and Secure Sockets Layer (SSL) protocols. It is also a general-purpose cryptography library.

popt

1.16

The popt library parses command line options.

python

3.9.9

The Python programming language.

rsync

3.2.3

An open source utility that provides fast incremental file transfer.

util-macros

1.19.3

This is a set of autoconf macros used by the configure.ac scripts in other Xorg modular packages, and is needed to generate new versions of their configure scripts with autoconf.

vasp

6.2.1

The Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics, from first principles.

xxhash

0.8.0

xxHash is an Extremely fast Hash algorithm, running at RAM speed limits. It successfully completes the SMHasher test suite which evaluates collision, dispersion and randomness qualities of hash functions. Code is highly portable, and hashes are identical on all platforms (little / big endian).

xz

5.2.5

XZ Utils is free general-purpose data compression software with high compression ratio. XZ Utils were written for POSIX-like systems, but also work on some not-so-POSIX systems. XZ Utils are the successor to LZMA Utils.

zlib

1.2.11

A free, general-purpose, legally unencumbered lossless data-compression library.

zstd

1.5.2

Zstandard, or zstd as short version, is a fast lossless compression algorithm, targeting real-time compression scenarios at zlib-level and better compression ratios.

abaqus

2021

The Abaqus Unified FEA product suite offers powerful and complete solutions for both routine and sophisticated engineering problems covering a vast spectrum of industrial applications. In the automotive industry engineering work groups are able to consider full vehicle loads, dynamic vibration, multibody systems, impact/crash, nonlinear static, thermal coupling, and acoustic-structural coupling using a common model data structure and integrated solver technology. Best-in-class companies are taking advantage of Abaqus Unified FEA to consolidate their processes and tools, reduce costs and inefficiencies, and gain a competitive advantage.

gaussian

09-D.01

Gaussian is a computer program for computational chemistry

star-ccm-plus

16.06.008_01

STAR-CCM+ (Computational Continuum Mechanics) CFD solver.

tecplot

2021r2

Tecplot 360 is a Computational Fluid Dynamics (CFD) and numerical simulation software package used in post-processing simulation results. It is also used in chemistry applications to visualize molecule structure by post-processing charge density data.

intel-oneapi-compilers

2022.0.2

Intel OneAPI compilers

nvhpc

22.2

The NVIDIA HPC SDK is a comprehensive suite of compilers, libraries and tools essential to maximizing developer productivity and the performance and portability of HPC applications. The NVIDIA HPC SDK C, C+, and Fortran compilers support GPU acceleration of HPC modeling and simulation applications with standard C+ and Fortran, OpenACC directives, and CUDA. GPU-accelerated math libraries maximize performance on common HPC algorithms, and optimized communications libraries enable standards-based multi-GPU and scalable systems programming. Performance profiling and debugging tools simplify porting and optimization of HPC applications.

intel-oneapi-ccl

2021.5.1

Intel oneAPI CCL.

intel-oneapi-dal

2021.5.3

Intel oneAPI DAL.

intel-oneapi-dnn

2022.0.2

Intel oneAPI DNN.

intel-oneapi-ipp

2021.5.2

Intel oneAPI IPP.

intel-oneapi-ippcp

2021.5.1

Intel oneAPI IPP Crypto.

intel-oneapi-mkl

2022.0.2

Intel oneAPI MKL.

intel-oneapi-mpi

2021.5.1

Intel oneAPI MPI.

intel-oneapi-tbb

2021.5.1

Intel oneAPI TBB.

intel-oneapi-vpl

2022.0.0

Intel oneAPI VPL.

rdma-core

39.0

RDMA core userspace libraries and daemons

abinit

9.6.1_gcc-9.4.0

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.

adios

1.13.1_gcc-9.4.0
1.13.1_intel-2021.5.0

The Adaptable IO System (ADIOS) provides a simple, flexible way for scientists to describe the data in their code that may need to be written, read, or processed outside of the running simulation.

adios2

2.7.1_gcc-9.4.0
2.7.1_intel-2021.5.0

The Adaptable Input Output System version 2, developed in the Exascale Computing Program

alsa-lib

1.2.3.2_gcc-9.4.0

The Advanced Linux Sound Architecture (ALSA) provides audio and MIDI functionality to the Linux operating system. alsa-lib contains the user space library that developers compile ALSA applications against.

ant

1.10.7_gcc-9.4.0

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

antlr

2.7.7_gcc-9.4.0

ANTLR (ANother Tool for Language Recognition) is a powerful parser generator for reading, processing, executing, or translating structured text or binary files. It's widely used to build languages, tools, and frameworks. From a grammar, ANTLR generates a parser that can build and walk parse trees.

ants

2.4.0_gcc-9.4.0

ANTs extracts information from complex datasets that include imaging. Paired with ANTsR (answer), ANTs is useful for managing, interpreting and visualizing multidimensional data. ANTs is popularly considered a state-of-the-art medical image registration and segmentation toolkit. ANTs depends on the Insight ToolKit (ITK), a widely used medical image processing library to which ANTs developers contribute.

armadillo

10.5.0_gcc-9.4.0

Armadillo is a high quality linear algebra library (matrix maths) for the C++ language, aiming towards a good balance between speed and ease of use.

arpack-ng

3.8.0_gcc-9.4.0

ARPACK-NG is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems.

asciidoc

9.1.0_gcc-9.4.0

A presentable text document format for writing articles, UNIX man pages and other small to medium sized documents.

assimp

5.2.2_gcc-9.4.0

Open Asset Import Library (Assimp) is a portable Open Source library to import various well-known 3D model formats in a uniform manner.

atk

2.36.0_gcc-9.4.0

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.

atompaw

4.1.1.0_gcc-9.4.0

A Projector Augmented Wave (PAW) code for generating atom-centered functions.

at-spi2-atk

2.38.0_gcc-9.4.0

The At-Spi2 Atk package contains a library that bridges ATK to At-Spi2 D-Bus service.

at-spi2-core

2.40.1_gcc-9.4.0

The At-Spi2 Core package provides a Service Provider Interface for the Assistive Technologies available on the GNOME platform and a library against which applications can be linked.

augustus

3.4.0_gcc-9.4.0

AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences

autoconf-archive

2019.01.06_gcc-9.4.0

The GNU Autoconf Archive is a collection of more than 500 macros for GNU Autoconf.

autodock-vina

1_1_2_gcc-9.4.0

AutoDock Vina is an open-source program for doing molecular docking

bamtools

2.5.1_gcc-9.4.0

C++ API & command-line toolkit for working with BAM data.

bart

0.7.00_gcc-9.4.0

BART: Toolbox for Computational Magnetic Resonance Imaging

bazel

4.0.0_gcc-9.4.0

Bazel is an open-source build and test tool similar to Make, Maven, and Gradle. It uses a human-readable, high-level build language. Bazel supports projects in multiple languages and builds outputs for multiple platforms. Bazel supports large codebases across multiple repositories, and large numbers of users.

bcftools

1.14_gcc-9.4.0

BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.

bdftopcf

1.0.5_gcc-9.4.0

bdftopcf is a font compiler for the X server and font server. Fonts in Portable Compiled Format can be read by any architecture, although the file is structured to allow one particular architecture to read them directly without reformatting. This allows fast reading on the appropriate machine, but the files are still portable (but read more slowly) on other machines.

bdw-gc

8.0.6_gcc-9.4.0

The Boehm-Demers-Weiser conservative garbage collector is a garbage collecting replacement for C malloc or C++ new.

beast1

1.10.4_gcc-9.4.0

BEAST is a cross-platform program for Bayesian analysis of molecular sequences using MCMC.

bedtools2

2.30.0_gcc-9.4.0

Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome.

berkeley-db

18.1.40_gcc-9.4.0

Oracle Berkeley DB

binutils

2.37_gcc-9.4.0

GNU binutils, which contain the linker, assembler, objdump and others

bismark

0.23.0_gcc-9.4.0

A tool to map bisulfite converted sequence reads and determine cytosine methylation states

blast-plus

2.12.0_gcc-9.4.0

Basic Local Alignment Search Tool.

blat

35_gcc-9.4.0

BLAT (BLAST-like alignment tool) is a pairwise sequence alignment algorithm.

boost

1.65.0_gcc-9.4.0
1.72.0_gcc-9.4.0
1.78.0_gcc-9.4.0
1.78.0_intel-2021.5.0

Boost provides free peer-reviewed portable C++ source libraries, emphasizing libraries that work well with the C++ Standard Library.

bowtie

1.3.0_gcc-9.4.0

Bowtie is an ultrafast, memory-efficient short read aligner for short DNA sequences (reads) from next-gen sequencers.

bowtie2

2.4.2_gcc-9.4.0

Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences

braker

2.1.6_gcc-9.4.0

BRAKER is a pipeline for unsupervised RNA-Seq-based genome annotation that combines the advantages of GeneMark-ET and AUGUSTUS

bwa

0.7.17_gcc-9.4.0

Burrow-Wheeler Aligner for pairwise alignment between DNA sequences.

bzip2

1.0.8_gcc-9.4.0
1.0.8_intel-2021.5.0

bzip2 is a freely available, patent free high-quality data compressor. It typically compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical compressors), whilst being around twice as fast at compression and six times faster at decompression.

cairo

1.16.0_gcc-9.4.0

Cairo is a 2D graphics library with support for multiple output devices.

c-ares

1.15.0_gcc-9.4.0

c-ares: A C library for asynchronous DNS requests

cbc

2.10.5_gcc-9.4.0

Cbc (Coin-or branch and cut) is an open-source mixed integer linear programming solver written in C++. It can be used as a callable library or using a stand-alone executable.

c-blosc

1.21.1_gcc-9.4.0
1.21.1_intel-2021.5.0

Blosc, an extremely fast, multi-threaded, meta-compressor library

cdo

2.0.4_gcc-9.4.0

CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.

cfitsio

4.0.0_gcc-9.4.0

CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format.

cgal

5.0.3_gcc-9.4.0

The Computational Geometry Algorithms Library (CGAL) is a C++ library that aims to provide easy access to efficient and reliable algorithms in computational geometry. CGAL is used in various areas needing geometric computation, such as geographic information systems, computer aided design, molecular biology, medical imaging, computer graphics, and robotics.

cgl

0.60.3_gcc-9.4.0

The COIN-OR Cut Generation Library (Cgl) is a collection of cut generators that can be used with other COIN-OR packages that make use of cuts, such as, among others, the linear solver Clp or the mixed integer linear programming solvers Cbc or BCP. Cgl uses the abstract class OsiSolverInterface (see Osi) to use or communicate with a solver. It does not directly call a solver.

check

0.12.0_gcc-9.4.0

Check is a unit testing framework for C. It features a simple interface for defining unit tests, putting little in the way of the developer. Tests are run in a separate address space, so both assertion failures and code errors that cause segmentation faults or other signals can be caught. Test results are reportable in the following: Subunit, TAP, XML, and a generic logging format.

cistem

1.0.0-beta_gcc-9.4.0

cisTEM is user-friendly software to process cryo-EM images of macromolecular complexes and obtain high-resolution 3D reconstructions from them.

clhep

2.4.5.1_gcc-9.4.0

CLHEP is a C++ Class Library for High Energy Physics.

clp

1.17.6_gcc-9.4.0

Clp (Coin-or linear programming) is an open-source linear programming solver written in C++.

cmaq

5.3.1_gcc-9.4.0

Code base for the U.S. EPA's Community Multiscale Air Quality Model (CMAQ).

cmdstan

2.30.1_gcc-9.4.0

CmdStan is the command line interface to Stan.

cnvnator

0.3.3_gcc-9.4.0

A tool for CNV discovery and genotyping from depth-of-coverage by mapped reads.

coinutils

2.11.4_gcc-9.4.0

CoinUtils is an open-source collection of classes and helper functions that are generally useful to multiple COIN-OR projects.

coreutils

8.32_gcc-9.4.0

The GNU Core Utilities are the basic file, shell and text manipulation utilities of the GNU operating system. These are the core utilities which are expected to exist on every operating system.

cp2k

9.1_gcc-9.4.0

CP2K is a quantum chemistry and solid state physics software package that can perform atomistic simulations of solid state, liquid, molecular, periodic, material, crystal, and biological systems

cpio

2.13_gcc-9.4.0

GNU cpio copies files into or out of a cpio or tar archive and the file system. The archive can be another file on the disk, a magnetic tape, or a pipe.

cppzmq

4.7.1_gcc-9.4.0

C++ binding for 0MQ

ctffind

4.1.14_gcc-9.4.0

Fast and accurate defocus estimation from electron micrographs.

cub

1.12.0-rc0_gcc-9.4.0

CUB is a C++ header library of cooperative threadblock primitives and other utilities for CUDA kernel programming.

cuda

11.4.4_gcc-9.4.0

CUDA is a parallel computing platform and programming model invented by NVIDIA. It enables dramatic increases in computing performance by harnessing the power of the graphics processing unit (GPU).

cudnn

8.2.4.15-11.4_gcc-9.4.0

NVIDIA cuDNN is a GPU-accelerated library of primitives for deep neural networks

cufflinks

2.2.1_gcc-9.4.0

Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples.

curl

7.78.0_gcc-9.4.0
7.81.0_gcc-9.4.0

cURL is an open source command line tool and library for transferring data with URL syntax

czmq

4.1.1_gcc-9.4.0

A C interface to the ZMQ library

damageproto

1.2.1_gcc-9.4.0

X Damage Extension.

darshan-runtime

3.3.1_gcc-9.4.0

Darshan (runtime) is a scalable HPC I/O characterization tool designed to capture an accurate picture of application I/O behavior, including properties such as patterns of access within files, with minimum overhead. DarshanRuntime package should be installed on systems where you intend to instrument MPI applications.

darshan-util

3.3.1_gcc-9.4.0

Darshan (util) is collection of tools for parsing and summarizing log files produced by Darshan (runtime) instrumentation. This package is typically installed on systems (front-end) where you intend to analyze log files produced by Darshan (runtime).

davix

0.7.6_gcc-9.4.0

High-performance file management over WebDAV/HTTP.

dbus

1.12.8_gcc-9.4.0

D-Bus is a message bus system, a simple way for applications to talk to one another. D-Bus supplies both a system daemon (for events such new hardware device printer queue ) and a per-user-login-session daemon (for general IPC needs among user applications). Also, the message bus is built on top of a general one-to-one message passing framework, which can be used by any two applications to communicate directly (without going through the message bus daemon).

dcm2niix

1.0.20210317_gcc-9.4.0

DICOM to NIfTI converter

diamond

2.0.11_gcc-9.4.0

DIAMOND is a sequence aligner for protein and translated DNA searches, designed for high performance analysis of big sequence data.

dicom3tools

1.00.snapshot.20210306100017_gcc-9.4.0

Command line utilities for creating, modifying, dumping and validating files of DICOM attributes, and conversion of proprietary image formats to DICOM. Can handle older ACR/NEMA format data, and some proprietary versions of that such as SPI.

docbook-xml

4.4_gcc-9.4.0
4.5_gcc-9.4.0

Docbook DTD XML files.

docbook-xsl

1.79.2_gcc-9.4.0-xml44
1.79.2_gcc-9.4.0-xml45

DocBook XSLT 1.0 Stylesheets.

double-conversion

3.1.5_gcc-9.4.0

This project (double-conversion) provides binary-decimal and decimal-binary routines for IEEE doubles.

doxygen

1.9.3_gcc-9.4.0
1.9.3_intel-2021.5.0

Doxygen is the de facto standard tool for generating documentation from annotated C++ sources, but it also supports other popular programming languages such as C, Objective-C, C#, PHP, Java, Python, IDL (Corba, Microsoft, and UNO/OpenOffice flavors), Fortran, VHDL, Tcl, and to some extent D..

dsfmt

2.2.5_gcc-9.4.0

Double precision SIMD-oriented Fast Mersenne Twister

eccodes

2.24.2_gcc-9.4.0

ecCodes is a package developed by ECMWF for processing meteorological data in GRIB (1/2), BUFR (3/4) and GTS header formats.

eigen

3.4.0_gcc-9.4.0

Eigen is a C++ template library for linear algebra matrices, vectors, numerical solvers, and related algorithms.

elfutils

0.186_gcc-9.4.0

elfutils is a collection of various binary tools such as eu-objdump, eu-readelf, and other utilities that allow you to inspect and manipulate ELF files. Refer to Table 5.Tools Included in elfutils for Red Hat Developer for a complete list of binary tools that are distributed with the Red Hat Developer Toolset version of elfutils.

esmf

8.2.0_gcc-9.4.0-hdf5110

The Earth System Modeling Framework (ESMF) is high-performance, flexible software infrastructure for building and coupling weather, climate, and related Earth science applications. The ESMF defines an architecture for composing complex, coupled modeling systems and includes data structures and utilities for developing individual models.

exonerate

2.4.0_gcc-9.4.0

Pairwise sequence alignment of DNA and proteins

expat

2.4.6_gcc-9.4.0

Expat is an XML parser library written in C.

fastqc

0.11.9_gcc-9.4.0

A quality control tool for high throughput sequence data.

fastx-toolkit

0.0.14_gcc-9.4.0

The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.

ffmpeg

4.4.1_gcc-9.4.0

FFmpeg is a complete, cross-platform solution to record, convert and stream audio and video.

fftw

3.3.10_gcc-9.4.0
3.3.10_intel-2021.5.0

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 (as well as of even/odd data, i.e. the discrete cosine/sine transforms or DCT/DST). We believe that FFTW, which is free software, should become the FFT library of choice for most applications.

fixesproto

5.0_gcc-9.4.0

X Fixes Extension.

flac

1.3.3_gcc-9.4.0

Encoder/decoder for the Free Lossless Audio Codec

flatbuffers

1.12.0_gcc-9.4.0

Memory Efficient Serialization Library

flex

2.6.4_gcc-9.4.0

Flex is a tool for generating scanners.

fltk

1.3.7_gcc-9.4.0

FLTK (pronounced 'fulltick') 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.

fontconfig

2.13.94_gcc-9.4.0

Fontconfig is a library for configuring/customizing font access

fontsproto

2.1.3_gcc-9.4.0

X Fonts Extension.

font-util

1.3.2_gcc-9.4.0

X.Org font package creation/installation utilities and fonts.

fox

1.6.57_gcc-9.4.0

FOX is a C++ based Toolkit for developing Graphical User Interfaces easily and effectively. It offers a wide, and growing, collection of Controls, and provides state of the art facilities such as drag and drop, selection, as well as OpenGL widgets for 3D graphical manipulation. FOX also implements icons, images, and user-convenience features such as status line help, and tooltips. Tooltips may even be used for 3D objects!

freeglut

3.2.2_gcc-9.4.0

FreeGLUT is a free-software/open-source alternative to the OpenGL Utility Toolkit (GLUT) library

freetype

2.11.1_gcc-9.4.0

FreeType is a freely available software library to render fonts. It is written in C, designed to be small, efficient, highly customizable, and portable while capable of producing high-quality output (glyph images) of most vector and bitmap font formats.

fribidi

1.0.5_gcc-9.4.0

GNU FriBidi: The Free Implementation of the Unicode Bidirectional Algorithm.

ftgl

2.4.0_gcc-9.4.0

Library to use arbitrary fonts in OpenGL applications.

fxdiv

2020-04-17_gcc-9.4.0

Header-only library for division via fixed-point multiplication by inverse.

g4abla

3.1_gcc-9.4.0

Geant4 data for nuclear shell effects in INCL/ABLA hadronic mode

g4emlow

7.13_gcc-9.4.0

Geant4 data files for low energy electromagnetic processes.

g4ensdfstate

2.3_gcc-9.4.0

Geant4 data for nuclides properties

g4incl

1.0_gcc-9.4.0

Geant4 data for evaluated particle cross-sections on natural composition of elements

g4ndl

4.6_gcc-9.4.0

Geant4 Neutron data files with thermal cross sections

g4particlexs

3.1.1_gcc-9.4.0

Geant4 data for evaluated particle cross-sections on natural composition of elements

g4photonevaporation

5.7_gcc-9.4.0

Geant4 data for photon evaporation

g4pii

1.3_gcc-9.4.0

Geant4 data for shell ionisation cross-sections

g4radioactivedecay

5.6_gcc-9.4.0

Geant4 data files for radio-active decay hadronic processes

g4realsurface

2.2_gcc-9.4.0

Geant4 data for measured optical surface reflectance

g4saiddata

2.0_gcc-9.4.0

Geant4 data from evaluated cross-sections in SAID data-base

gate

9.1_gcc-9.4.0

Simulations of Preclinical and Clinical Scans in Emission Tomography, Transmission Tomography and Radiation Therapy

gatepet2stir

1.3.2_gcc-9.4.0

A QT/C++ application to convert GATE geometries to STIR format.

gatetools

0.11.2_gcc-9.4.0

Python tools for GATE, see https://github.com/OpenGATE/Gate

gatk

4.2.2.0_gcc-9.4.0

Genome Analysis Toolkit Variant Discovery in High-Throughput Sequencing Data

gdal

2.4.4_gcc-9.4.0
3.4.1_gcc-9.4.0-proj7-python
3.4.1_gcc-9.4.0-proj8

GDAL (Geospatial Data Abstraction Library) is a translator library for raster and vector geospatial data formats that is released under an X/MIT style Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single raster abstract data model and vector abstract data model to the calling application for all supported formats. It also comes with a variety of useful command line utilities for data translation and processing.

gdk-pixbuf

2.42.6_gcc-9.4.0

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.

geant4

10.7.3_gcc-9.4.0

Geant4 is a toolkit for the simulation of the passage of particles through matter. Its areas of application include high energy, nuclear and accelerator physics, as well as studies in medical and space science.

geant4-data

10.7.3_gcc-9.4.0

A bundle package to hold Geant4 data packages

genemark-et

4.65_gcc-9.4.0

Gene Prediction in Bacteria, archaea, Metagenomes and Metatranscriptomes. When downloaded this file is named the same for all versions. Spack will search your current directory for the download file. Alternatively, add this file to a mirror so that Spack can find it. For instructions on how to set up a mirror, see https://spack.readthedocs.io/en/latest/mirrors.html

genrich

0.6_gcc-9.4.0

Genrich is a peak-caller for genomic enrichment assays.

geos

3.9.1_gcc-9.4.0

GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS). As such, it aims to contain the complete functionality of JTS in C++. This includes all the OpenGIS Simple Features for SQL spatial predicate functions and spatial operators, as well as specific JTS enhanced topology functions.

gettext

0.21_gcc-9.4.0

GNU internationalization (i18n) and localization (l10n) library.

gflags

2.2.2_gcc-9.4.0

The gflags package contains a C++ library that implements commandline flags processing. It includes built-in support for standard types such as string and the ability to define flags in the source file in which they are used. Online documentation available at: https://gflags.github.io/gflags/

ghostscript

9.54.0_gcc-9.4.0

An interpreter for the PostScript language and for PDF.

ghostscript-fonts

8.11_gcc-9.4.0

Ghostscript Fonts

giflib

5.2.1_gcc-9.4.0

The GIFLIB project maintains the giflib service library, which has been pulling images out of GIFs since 1989.

git

2.34.1_gcc-9.4.0

Git is a free and open source distributed version control system designed to handle everything from small to very large projects with speed and efficiency.

gl2ps

1.4.2_gcc-9.4.0

GL2PS is a C library providing high quality vector output for any OpenGL application.

glew

2.1.0_gcc-9.4.0

The OpenGL Extension Wrangler Library.

glib

2.70.4_gcc-9.4.0

GLib provides the core application building blocks for libraries and applications written in C.

glpk

4.65_gcc-9.4.0

The GLPK (GNU Linear Programming Kit) package is intended for solving large-scale linear programming (LP), mixed integer programming (MIP), and other related problems. It is a set of routines written in ANSI C and organized in the form of a callable library.

glproto

1.4.17_gcc-9.4.0

OpenGL Extension to the X Window System.

gmp

6.2.1_gcc-9.4.0

GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating-point numbers.

gmt

6.2.0_gcc-9.4.0

GMT (Generic Mapping Tools) is an open source collection of about 80 command-line tools for manipulating geographic and Cartesian data sets (including filtering, trend fitting, gridding, projecting, etc.) and producing PostScript illustrations ranging from simple x-y plots via contour maps to artificially illuminated surfaces and 3D perspective views.

gnuplot

5.4.2_gcc-9.4.0

Gnuplot is a portable command-line driven graphing utility for Linux, OS/2, MS Windows, OSX, VMS, and many other platforms. The source code is copyrighted but freely distributed (i.e., you don't have to pay for it). It was originally created to allow scientists and students to visualize mathematical functions and data interactively, but has grown to support many non-interactive uses such as web scripting. It is also used as a plotting engine by third-party applications like Octave. Gnuplot has been supported and under active development since 1986

gnutls

3.6.15_gcc-9.4.0

GnuTLS is a secure communications library implementing the SSL, TLS and DTLS protocols and technologies around them. It provides a simple C language application programming interface (API) to access the secure communications protocols as well as APIs to parse and write X.509, PKCS #12, OpenPGP and other required structures. It is aimed to be portable and efficient with focus on security and interoperability.

go

1.15.13_gcc-9.4.0

The golang compiler and build environment

gobject-introspection

1.56.1_gcc-9.4.0

The GObject Introspection is used to describe the program APIs and collect them in a uniform, machine readable format.Cairo is a 2D graphics library with support for multiple output

go-bootstrap

1.4-bootstrap-20171003_gcc-9.4.0

Old C-bootstrapped go to bootstrap real go

googletest

1.10.0_gcc-9.4.0

Google test framework for C++. Also called gtest.

gperf

3.1_gcc-9.4.0

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.

gperftools

2.9.1_gcc-9.4.0

Google's fast malloc/free implementation, especially for multi-threaded applications. Contains tcmalloc, heap-checker, heap-profiler, and cpu-profiler.

gpu-burn

1.1_gcc-9.4.0

Multi-GPU CUDA stress test.

graphicsmagick

1.3.34_gcc-9.4.0

GraphicsMagick is the swiss army knife of image processing.

graphite2

1.3.13_gcc-9.4.0

Graphite is a system that can be used to create 'smart fonts' capable of displaying writing systems with various complex behaviors. A smart font contains not only letter shapes but also additional instructions indicating how to combine and position the letters in complex ways.

graphviz

2.49.0_gcc-9.4.0

Graph Visualization Software

gromacs

2021.5_gcc-9.4.0

GROMACS (GROningen MAchine for Chemical Simulations) is a molecular dynamics package primarily designed for simulations of proteins, lipids and nucleic acids. It was originally developed in the Biophysical Chemistry department of University of Groningen, and is now maintained by contributors in universities and research centers across the world.

gsl

2.7_gcc-9.4.0

The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. It is free software under the GNU General Public License. The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting. There are over 1000 functions in total with an extensive test suite.

gtkplus

3.24.29_gcc-9.4.0

The GTK+ package contains libraries used for creating graphical user interfaces for applications.

guile

2.2.6_gcc-9.4.0

Guile is the GNU Ubiquitous Intelligent Language for Extensions, the official extension language for the GNU operating system.

gzip

1.11_gcc-9.4.0

GNU Gzip is a popular data compression program originally written by Jean-loup Gailly for the GNU project.

harfbuzz

2.9.1_gcc-9.4.0

The Harfbuzz package contains an OpenType text shaping engine.

hdf

4.2.15_gcc-9.4.0
4.2.15_intel-2021.5.0

HDF4 (also known as HDF) is a library and multi-object file format for storing and managing data between machines.

hdf5

1.10.8_gcc-9.4.0
1.10.8_gcc-9.4.0-mpi
1.10.8_intel-2021.5.0
1.10.8_intel-2021.5.0-mpi
1.12.1_gcc-9.4.0
1.12.1_gcc-9.4.0-mpi
1.12.1_intel-2021.5.0
1.12.1_intel-2021.5.0-mpi

HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data.

hdf-eos2

2.20v1.00_gcc-9.4.0

HDF-EOS (Hierarchical Data Format - Earth Observing System) is a self-describing file format based upon HDF for standard data products that are derived from EOS missions. HDF-EOS2 is based upon HDF4.

hdf-eos5

5.1.16_gcc-9.4.0

HDF-EOS (Hierarchical Data Format - Earth Observing System) is a self-describing file format based upon HDF for standard data products that are derived from EOS missions. HDF-EOS5 is based upon HDF5.

heasoft

6.29_gcc-9.4.0

A Unified Release of the FTOOLS and XANADU Software Packages.

hepmc

2.06.11_gcc-9.4.0

The HepMC package is an object oriented, C++ event record for High Energy Physics Monte Carlo generators and simulation.

hepmc3

3.2.4_gcc-9.4.0

The HepMC package is an object oriented, C++ event record for High Energy Physics Monte Carlo generators and simulation.

highfive

2.4.1_gcc-9.4.0
2.4.1_gcc-9.4.0-mpi

HighFive - Header only C++ HDF5 interface

hmmer

3.3.2_gcc-9.4.0

HMMER is used for searching sequence databases for sequence homologs, and for making sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs).

hpl

2.3_gcc-9.4.0

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.

htslib

1.13_gcc-9.4.0
1.14_gcc-9.4.0

C library for high-throughput sequencing data formats.

hwloc

2.7.0_gcc-9.4.0
2.7.0_intel-2021.5.0

The Hardware Locality (hwloc) software project.

hypre

2.23.0_gcc-9.4.0
2.23.0_intel-2021.5.0
2.24.0_gcc-9.4.0
2.24.0_intel-2021.5.0

Hypre is a library of high performance preconditioners that features parallel multigrid methods for both structured and unstructured grid problems.

icu4c

67.1_gcc-9.4.0

ICU is a mature, widely used set of C/C++ and Java libraries providing Unicode and Globalization support for software applications. ICU4C is the C/C++ interface.

id3lib

3.8.3_gcc-9.4.0

Library for manipulating ID3v1 and ID3v2 tags

ilmbase

2.3.0_gcc-9.4.0

OpenEXR ILM Base libraries (high dynamic-range image file format)

imagemagick

7.0.8-7_gcc-9.4.0

ImageMagick is a software suite to create, edit, compose, or convert bitmap images.

imake

1.0.7_gcc-9.4.0

The imake build system.

infernal

1.1.2_gcc-9.4.0

Infernal (INFERence of RNA ALignment) is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs).

inputproto

2.3.2_gcc-9.4.0

X Input Extension.

intel-oneapi-mkl

2022.0.2_gcc-9.4.0
2022.0.2_intel-2021.5.0

Intel oneAPI MKL.

intel-oneapi-tbb

2021.5.1_gcc-9.4.0

Intel oneAPI TBB.

intel-xed

12.0.1_gcc-9.4.0

The Intel X86 Encoder Decoder library for encoding and decoding x86 machine instructions (64- and 32-bit). Also includes libxed-ild, a lightweight library for decoding the length of an instruction.

interproscan

4.8_gcc-9.4.0
5.38-76.0_gcc-9.4.0

InterProScan is the software package that allows sequences (protein and nucleic) to be scanned against InterPro's signatures. Signatures are predictive models, provided by several different databases, that make up the InterPro consortium.

intltool

0.51.0_gcc-9.4.0

intltool is a set of tools to centralize translation of many different file formats using GNU gettext-compatible PO files.

itk

5.2.1_gcc-9.4.0

The Insight Toolkit (ITK) is an open-source, cross-platform toolkit for N-dimensional scientific image processing, segmentation, and registration.

jags

4.3.0_gcc-9.4.0

JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation not wholly unlike BUGS

jasper

2.0.32_gcc-9.4.0

Library for manipulating JPEG-2000 images

jellyfish

2.2.7_gcc-9.4.0

JELLYFISH is a tool for fast, memory-efficient counting of k-mers in DNA.

jq

1.6_gcc-9.4.0

jq is a lightweight and flexible command-line JSON processor.

json-c

0.15_gcc-9.4.0

A JSON implementation in C.

jsoncpp

1.9.4_gcc-9.4.0

JsonCpp is a C++ library that allows manipulating JSON values, including serialization and deserialization to and from strings. It can also preserve existing comment in unserialization/serialization steps, making it a convenient format to store user input files.

julia

1.7.2_gcc-9.4.0

The Julia Language: A fresh approach to technical computing

kallisto

0.48.0_gcc-9.4.0

kallisto is a program for quantifying abundances of transcripts from RNA-Seq data.

kbproto

1.0.7_gcc-9.4.0

X Keyboard Extension.

kim-api

2.2.1_gcc-9.4.0

OpenKIM is an online framework for making molecular simulations reliable, reproducible, and portable. Computer implementations of inter-atomic models are archived in OpenKIM, verified for coding integrity, and tested by computing their predictions for a variety of material properties. Models conforming to the KIM application programming interface (API) work seamlessly with major simulation codes that have adopted the KIM API standard.

kokkos

3.5.00_gcc-9.4.0

Kokkos implements a programming model in C++ for writing performance portable applications targeting all major HPC platforms.

krb5

1.19.2_gcc-9.4.0
1.19.2_intel-2021.5.0

Network authentication protocol

lammps

20220107_gcc-9.4.0

LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel Simulator. This package uses patch releases, not stable release. See https://github.com/spack/spack/pull/5342 for a detailed discussion.

laszip

3.4.1_gcc-9.4.0

Free and lossless LiDAR compression

latte

1.2.2_gcc-9.4.0

Open source density functional tight binding molecular dynamics.

lcms

2.9_gcc-9.4.0

Little cms is a color management library. Implements fast transforms between ICC profiles. It is focused on speed, and is portable across several platforms (MIT license).

leptonica

1.81.0_gcc-9.4.0

Leptonica is an open source library containing software that is broadly useful for image processing and image analysis applications.

libaec

1.0.5_gcc-9.4.0
1.0.5_intel-2021.5.0

Libaec provides fast lossless compression of 1 up to 32 bit wide signed or unsigned integers (samples). It implements Golomb-Rice compression method under the BSD license and includes a free drop-in replacement for the SZIP library.

libaio

0.3.110_gcc-9.4.0

Linux native Asynchronous I/O interface library.

libao

1.2.2_gcc-9.4.0

A Cross-platform Audio Library.

libarchive

3.5.2_gcc-9.4.0

libarchive: C library and command-line tools for reading and writing tar, cpio, zip, ISO, and other archive formats.

libatomic-ops

7.6.12_gcc-9.4.0

This package provides semi-portable access to hardware-provided atomic memory update operations on a number architectures.

libbeagle

3.1.2_gcc-9.4.0

Beagle performs genotype calling, genotype phasing, imputation of ungenotyped markers, and identity-by-descent segment detection.

libblastrampoline

3.1.0_gcc-9.4.0

Using PLT trampolines to provide a BLAS and LAPACK demuxing library.

libbsd

0.11.5_gcc-9.4.0

This library provides useful functions commonly found on BSD systems, and lacking on others like GNU systems, thus making it easier to port projects with strong BSD origins, without needing to embed the same code over and over again on each project.

libcerf

1.3_gcc-9.4.0

A self-contained C library providing complex error functions, based on Faddeeva's plasma dispersion function w(z). Also provides Dawson's integral and Voigt's convolution of a Gaussian and a Lorentzian

libcroco

0.6.13_gcc-9.4.0

Libcroco is a standalone css2 parsing and manipulation library.

libdeflate

1.7_gcc-9.4.0

Heavily optimized library for DEFLATE/zlib/gzip compression and decompression

libdrm

2.4.110_gcc-9.4.0

A userspace library for accessing the DRM, direct rendering manager, on Linux, BSD and other systems supporting the ioctl interface.

libedit

3.1-20210216_gcc-9.4.0

An autotools compatible port of the NetBSD editline library

libepoxy

1.4.3_gcc-9.4.0

Epoxy is a library for handling OpenGL function pointer management for you.

libevent

2.1.12_gcc-9.4.0
2.1.12_intel-2021.5.0

The libevent API provides a mechanism to execute a callback function when a specific event occurs on a file descriptor or after a timeout has been reached. Furthermore, libevent also support callbacks due to signals or regular timeouts.

libfabric

1.14.0_gcc-9.4.0
1.14.0_intel-2021.5.0

The Open Fabrics Interfaces (OFI) is a framework focused on exporting fabric communication services to applications.

libffi

3.4.2_gcc-9.4.0
3.4.2_intel-2021.5.0

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.

libfontenc

1.1.3_gcc-9.4.0

libfontenc - font encoding library.

libgcrypt

1.9.4_gcc-9.4.0

Cryptographic library based on the code from GnuPG.

libgd

2.2.4_gcc-9.4.0

GD is an open source code library for the dynamic creation of images by programmers. GD is written in C, and 'wrappers' are available for Perl, PHP and other languages. GD creates PNG, JPEG, GIF, WebP, XPM, BMP images, among other formats. GD is commonly used to generate charts, graphics, thumbnails, and most anything else, on the fly. While not restricted to use on the web, the most common applications of GD involve website development.

libgeotiff

1.4.3_gcc-9.4.0
1.6.0_gcc-9.4.0-proj7
1.6.0_gcc-9.4.0-proj8

GeoTIFF represents an effort by over 160 different remote sensing, GIS, cartographic, and surveying related companies and organizations to establish a TIFF based interchange format for georeferenced raster imagery.

libgit2

1.1.1_gcc-9.4.0

libgit2 is a portable, pure C implementation of the Git core methods provided as a re-entrant linkable library with a solid API, allowing you to write native speed custom Git applications in any language which supports C bindings.

libgpg-error

1.43_gcc-9.4.0

Common error values for all GnuPG components.

libgpuarray

0.7.6_gcc-9.4.0

Make a common GPU ndarray(n dimensions array) that can be reused by all projects that is as future proof as possible, while keeping it easy to use for simple need/quick test.

libgtextutils

0.7_gcc-9.4.0

Gordon's Text utils Library.

libice

1.0.9_gcc-9.4.0

libICE - Inter-Client Exchange Library.

libiconv

1.16_gcc-9.4.0
1.16_intel-2021.5.0

GNU libiconv provides an implementation of the iconv() function and the iconv program for character set conversion.

libid3tag

0.15.1b_gcc-9.4.0

library for id3 tagging

libidn2

2.3.0_gcc-9.4.0

Libidn2 is a free software implementation of IDNA2008, Punycode and TR46. Its purpose is to encode and decode internationalized domain names.

libint

2.6.0_gcc-9.4.0

Libint is a high-performance library for computing Gaussian integrals in quantum mechanics.

libjpeg-turbo

2.1.0_gcc-9.4.0
2.1.0_intel-2021.5.0

libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to accelerate baseline JPEG compression and decompression.

liblas

1.8.1_gcc-9.4.0

libLAS is a C/C++ library for reading and writing the very common LAS LiDAR format.

libmd

1.0.4_gcc-9.4.0

This library provides message digest functions found on BSD systems either on their libc (NetBSD, OpenBSD) or libmd (FreeBSD, DragonflyBSD, macOS, Solaris) libraries and lacking on others like GNU systems.

libmng

2.0.3_gcc-9.4.0

THE reference library for reading, displaying, writing and examining Multiple-Image Network Graphics. MNG is the animation extension to the popular PNG image format.

libogg

1.3.5_gcc-9.4.0

Ogg is a multimedia container format, and the native file and stream format for the Xiph.org multimedia codecs.

libpaper

1.1.28_gcc-9.4.0

The paper library and accompanying files are intended to provide a simple way for applications to take actions based on a system- or user-specified paper size.

libpciaccess

0.16_gcc-9.4.0
0.16_intel-2021.5.0

Generic PCI access library.

libpng

1.6.37_gcc-9.4.0
1.6.37_intel-2021.5.0

libpng is the official PNG reference library.

libpthread-stubs

0.4_gcc-9.4.0

The libpthread-stubs package provides weak aliases for pthread functions not provided in libc or otherwise available by default.

librsvg

2.51.0_gcc-9.4.0

Library to render SVG files using Cairo

libsm

1.2.3_gcc-9.4.0

libSM - X Session Management Library.

libsndfile

1.0.28_gcc-9.4.0

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. It is released in source code format under the Gnu Lesser General Public License.

libsodium

1.0.18_gcc-9.4.0

Sodium is a modern, easy-to-use software library for encryption, decryption, signatures, password hashing and more.

libssh2

1.10.0_gcc-9.4.0

libssh2 is a client-side C library implementing the SSH2 protocol

libtiff

4.3.0_gcc-9.4.0

LibTIFF - Tag Image File Format (TIFF) Library and Utilities.

libtirpc

1.2.6_gcc-9.4.0
1.2.6_intel-2021.5.0

Libtirpc is a port of Suns Transport-Independent RPC library to Linux.

libtool

2.4.6_gcc-9.4.0

libtool – library building part of autotools.

libunistring

0.9.10_gcc-9.4.0

This library provides functions for manipulating Unicode strings and for manipulating C strings according to the Unicode standard.

libunwind

1.5.0_gcc-9.4.0

A portable and efficient C programming interface (API) to determine the call-chain of a program.

libvorbis

1.3.7_gcc-9.4.0

Ogg Vorbis is a fully open, non-proprietary, patent-and-royalty-free, general-purpose compressed audio format for mid to high quality (8kHz- 48.0kHz, 16+ bit, polyphonic) audio and music at fixed and variable bitrates from 16 to 128 kbps/channel.

libwebp

1.2.0_gcc-9.4.0

WebP is a modern image format that provides superior lossless and lossy compression for images on the web. Using WebP, webmasters and web developers can create smaller, richer images that make the web faster.

libwhich

1.1.0_gcc-9.4.0

Libwhich: the functionality of which for libraries.

libx11

1.7.0_gcc-9.4.0

libX11 - Core X11 protocol client library.

libxau

1.0.8_gcc-9.4.0

The libXau package contains a library implementing the X11 Authorization Protocol. This is useful for restricting client access to the display.

libxaw

1.0.13_gcc-9.4.0

Xaw is the X Athena Widget Set. Xaw is a widget set based on the X Toolkit Intrinsics (Xt) Library.

libxc

5.1.7_gcc-9.4.0

Libxc is a library of exchange-correlation functionals for density-functional theory.

libxcb

1.14_gcc-9.4.0

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.

libxcursor

1.1.14_gcc-9.4.0

libXcursor - X Window System Cursor management library.

libxdamage

1.1.4_gcc-9.4.0

This package contains the library for the X Damage extension.

libxdmcp

1.1.2_gcc-9.4.0

libXdmcp - X Display Manager Control Protocol library.

libxext

1.3.3_gcc-9.4.0

libXext - library for common extensions to the X11 protocol.

libxfixes

5.0.2_gcc-9.4.0

This package contains header files and documentation for the XFIXES extension. Library and server implementations are separate.

libxfont

1.5.2_gcc-9.4.0

libXfont provides the core of the legacy X11 font system, handling the index files (fonts.dir, fonts.alias, fonts.scale), the various font file formats, and rasterizing them. It is used by the X servers, the X Font Server (xfs), and some font utilities (bdftopcf for instance), but should not be used by normal X11 clients. X11 clients access fonts via either the new API's in libXft, or the legacy API's in libX11.

libxft

2.3.2_gcc-9.4.0

X FreeType library.

libxi

1.7.6_gcc-9.4.0

libXi - library for the X Input Extension.

libxinerama

1.1.3_gcc-9.4.0

libXinerama - API for Xinerama extension to X11 Protocol.

libxkbcommon

0.8.2_gcc-9.4.0

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.

libxkbfile

1.0.9_gcc-9.4.0

XKB file handling routines.

libxml2

2.9.12_gcc-9.4.0
2.9.12_intel-2021.5.0

Libxml2 is the XML C parser and toolkit developed for the Gnome project (but usable outside of the Gnome platform), it is free software available under the MIT License.

libxmu

1.1.2_gcc-9.4.0

This library contains miscellaneous utilities and is not part of the Xlib standard. It contains routines which only use public interfaces so that it may be layered on top of any proprietary implementation of Xlib or Xt.

libxpm

3.5.12_gcc-9.4.0

libXpm - X Pixmap (XPM) image file format library.

libxrandr

1.5.0_gcc-9.4.0

libXrandr - X Resize, Rotate and Reflection extension library.

libxrender

0.9.10_gcc-9.4.0

libXrender - library for the Render Extension to the X11 protocol.

libxscrnsaver

1.2.2_gcc-9.4.0

XScreenSaver - X11 Screen Saver extension client library

libxslt

1.1.33_gcc-9.4.0

Libxslt is the XSLT C library developed for the GNOME project. XSLT itself is a an XML language to define transformation for XML. Libxslt is based on libxml2 the XML C library developed for the GNOME project. It also implements most of the EXSLT set of processor-portable extensions functions and some of Saxon's evaluate and expressions extensions.

libxsmm

1.17_gcc-9.4.0

Library for specialized dense and sparse matrix operations, and deep learning primitives.

libxt

1.1.5_gcc-9.4.0

libXt - X Toolkit Intrinsics library.

libxtst

1.2.2_gcc-9.4.0

libXtst provides the Xlib-based client API for the XTEST & RECORD extensions.

libxxf86vm

1.1.4_gcc-9.4.0

libXxf86vm - Extension library for the XFree86-VidMode X extension.

libyaml

0.2.5_gcc-9.4.0

A C library for parsing and emitting YAML.

libzmq

4.3.4_gcc-9.4.0

The ZMQ networking/concurrency library and core API

llvm

11.0.1_gcc-9.4.0

The LLVM Project is a collection of modular and reusable compiler and toolchain technologies. Despite its name, LLVM has little to do with traditional virtual machines, though it does provide helpful libraries that can be used to build them. The name 'LLVM' itself is not an acronym; it is the full name of the project.

lmdb

0.9.29_gcc-9.4.0

Symas LMDB is an extraordinarily fast, memory-efficient database we developed for the Symas OpenLDAP Project. With memory-mapped files, it has the read performance of a pure in-memory database while retaining the persistence of standard disk-based databases.

lp-solve

5.5.2.11_gcc-9.4.0

lp_solve is a Mixed Integer Linear Programming (MILP) solver.

lz4

1.9.3_gcc-9.4.0
1.9.3_intel-2021.5.0

LZ4 is lossless compression algorithm, providing compression speed at 400 MB/s per core, scalable with multi-cores CPU. It also features an extremely fast decoder, with speed in multiple GB/s per core, typically reaching RAM speed limits on multi-core systems.

lzo

2.10_gcc-9.4.0

Real-time data compression library

mafft

7.481_gcc-9.4.0

MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <~200 sequences), FFT-NS-2 (fast; for alignment of <~30,000 sequences), etc.

magma

2.6.1_gcc-9.4.0

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.

makedepend

1.0.5_gcc-9.4.0

makedepend - create dependencies in makefiles.

maker

3.01.03_gcc-9.4.0

MAKER is a portable and easily configurable genome annotation pipeline. It's purpose is to allow smaller eukaryotic and prokaryotic genomeprojects to independently annotate their genomes and to create genome databases. MAKER identifies repeats, aligns ESTs and proteins to a genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence-based quality values. MAKER is also easily trainable: outputs of preliminary runs can be used to automatically retrain its gene prediction algorithm, producing higher quality gene-models on subsequent runs. MAKER's inputs are minimal and its ouputs can be directly loaded into a GMOD database. They can also be viewed in the Apollo genome browser; this feature of MAKER provides an easy means to annotate, view and edit individual contigs and BACs without the overhead of a database. MAKER should prove especially useful for emerging model organism projects with minimal bioinformatics expertise and computer resources.

mariadb-c-client

3.2.6_gcc-9.4.0

MariaDB turns data into structured information in a wide array of applications, ranging from banking to websites. It is an enhanced, drop-in replacement for MySQL. MariaDB is used because it is fast, scalable and robust, with a rich ecosystem of storage engines, plugins and many other tools make it very versatile for a wide variety of use cases. This package comprises only the standalone 'C Connector', which enables connections to MariaDB and MySQL servers.

maven

3.8.4_gcc-9.4.0

Apache Maven is a software project management and comprehension tool.

mbedtls

2.24.0_gcc-9.4.0

mbed TLS (formerly known as PolarSSL) makes it trivially easy for developers to include cryptographic and SSL/TLS capabilities in their (embedded) products, facilitating this functionality with a minimal coding footprint.

mesa

21.3.1_gcc-9.4.0

Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics.

mesa-glu

9.0.1_gcc-9.4.0

This package provides the Mesa OpenGL Utility library.

mesquite

2.99_gcc-9.4.0

Mesquite (Mesh Quality Improvement Toolkit) is designed to provide a stand-alone, portable, comprehensive suite of mesh quality improvement algorithms and components that can be used to construct custom quality improvement algorithms. Mesquite provides a robust and effective mesh improvement toolkit that allows both meshing researchers application scientists to benefit from the latest developments in mesh quality control and improvement.

metis

5.1.0_gcc-9.4.0
5.1.0_intel-2021.5.0

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.

mfem

4.3.0_gcc-9.4.0
4.3.0_intel-2021.5.0

Free, lightweight, scalable C++ library for finite element methods.

mkfontdir

1.0.7_gcc-9.4.0

mkfontdir creates the fonts.dir files needed by the legacy X server core font system. The current implementation is a simple wrapper script around the mkfontscale program, which must be built and installed first.

mkfontscale

1.1.2_gcc-9.4.0

mkfontscale creates the fonts.scale and fonts.dir index files used by the legacy X11 font system.

mono

6.12.0.122_gcc-9.4.0

Mono is a software platform designed to allow developers to easily create cross platform applications. It is an open source implementation of Microsoft's .NET Framework based on the ECMA standards for C# and the Common Language Runtime.

motioncor2

1.4.7_gcc-9.4.0

MotionCor2 is a multi-GPU program that corrects beam-induced sample motion recorded on dose fractionated movie stacks. It implements a robust iterative alignment algorithm that delivers precise measurement and correction of both global and non-uniform local motions at single pixel level, suitable for both single-particle and tomographic images. MotionCor2 is sufficiently fast to keep up with automated data collection.

mpc

1.2.1_gcc-9.4.0

Gnu Mpc is a C library for the arithmetic of complex numbers with arbitrarily high precision and correct rounding of the result.

mpfi

1.5.4_gcc-9.4.0

Library for arbitrary precision interval arithmetic based on MPFR

mpfr

4.1.0_gcc-9.4.0

The MPFR library is a C library for multiple-precision floating-point computations with correct rounding.

mumax

3.10_gcc-9.4.0

GPU accelerated micromagnetic simulator.

mumps

5.4.0_gcc-9.4.0
5.4.0_intel-2021.5.0

MUMPS: a MUltifrontal Massively Parallel sparse direct Solver

muparser

2.2.6.1_gcc-9.4.0

C++ math expression parser library.

mysqlpp

3.2.5_gcc-9.4.0

MySQL++ is a C++ wrapper for MySQL and MariaDB C APIs. It is built on the same principles as the Standard C++ Library to make dealing with the database as easy as dealing with std containers. MySQL++ also provides facilities that let you avoid the most repetitive sorts of SQL within your own code, providing native C++ interfaces for these common tasks.

nasm

2.15.05_gcc-9.4.0
2.15.05_intel-2021.5.0

NASM (Netwide Assembler) is an 80x86 assembler designed for portability and modularity. It includes a disassembler as well.

ncbi-rmblastn

2.11.0_gcc-9.4.0

RMBlast search engine for NCBI

nccl

2.11.4-1_gcc-9.4.0

Optimized primitives for collective multi-GPU communication.

ncl

6.6.2_gcc-9.4.0-hdf5110

NCL is an interpreted language designed specifically for scientific data analysis and visualization. Supports NetCDF 3/4, GRIB 1/2, HDF 4/5, HDF-EOD 2/5, shapefile, ASCII, binary. Numerous analysis functions are built-in.

nco

5.0.1_gcc-9.4.0

The NCO toolkit manipulates and analyzes data stored in netCDF-accessible formats

ncurses

6.2_gcc-9.4.0
6.2_intel-2021.5.0

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.

ncview

2.1.8_gcc-9.4.0

Simple viewer for NetCDF files.

netcdf-c

4.8.1_gcc-9.4.0-hdf5110
4.8.1_gcc-9.4.0
4.8.1_intel-2021.5.0

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. This is the C distribution.

netcdf-cxx4

4.3.1_gcc-9.4.0
4.3.1_intel-2021.5.0

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. This is the C++ distribution.

netcdf-fortran

4.5.3_gcc-9.4.0-hdf5110
4.5.3_gcc-9.4.0
4.5.3_intel-2021.5.0

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. This is the Fortran distribution.

netlib-scalapack

2.1.0_gcc-9.4.0
2.1.0_intel-2021.5.0

ScaLAPACK is a library of high-performance linear algebra routines for parallel distributed memory machines

nettle

3.4.1_gcc-9.4.0

The Nettle package contains the low-level cryptographic library that is designed to fit easily in many contexts.

nextflow

21.10.6_gcc-9.4.0

Data-driven computational pipelines.

nghttp2

1.44.0_gcc-9.4.0

nghttp2 is an implementation of HTTP/2 and its header compression algorithm HPACK in C.

ngmerge

0.3_gcc-9.4.0

Merging paired-end reads and removing adapters.

nlohmann-json

3.10.5_gcc-9.4.0

JSON for Modern C++

nlopt

2.7.0_gcc-9.4.0

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.

numactl

2.0.14_gcc-9.4.0
2.0.14_intel-2021.5.0

NUMA support for Linux

ocaml

4.13.1_gcc-9.4.0

OCaml is an industrial strength programming language supporting functional, imperative and object-oriented styles

octave

6.4.0_gcc-9.4.0

GNU Octave is a high-level language, primarily intended for numerical computations.

octave-arduino

0.2.0_gcc-9.4.0

Provides an Octave look-alike implementation of the Arduino extension for Matlab.

octave-control

3.2.0_gcc-9.4.0

Computer-Aided Control System Design (CACSD) Tools for GNU Octave, based on the proven SLICOT Library

octave-gsl

2.1.1_gcc-9.4.0

Octave bindings to the GNU Scientific Library

octave-instrctl

0.3.1_gcc-9.4.0

Instrument-Control is a package for interfacing the outside world of hardware via Serial, i2c or Parallel interfaces.

octave-io

2.6.3_gcc-9.4.0

The IO package is part of the Octave Forge project and provides input/output from/in external formats.

octave-signal

1.4.1_gcc-9.4.0

Signal processing tools, including filtering, windowing and display functions.

octave-splines

1.3.3_gcc-9.4.0

Additional spline functions.

octave-statistics

1.4.2_gcc-9.4.0

Additional statistics functions for Octave.

octave-symbolic

2.9.0_gcc-9.4.0

Adds symbolic calculation features to GNU Octave. These include common Computer Algebra System tools such as algebraic operations, calculus, equation solving, Fourier and Laplace transforms, variable precision arithmetic and other features. Compatibility with other symbolic toolboxes is intended.

oniguruma

6.9.4_gcc-9.4.0

Regular expression library.

opa-psm2

11.2.206_gcc-9.4.0
11.2.206_intel-2021.5.0

Omni-Path Performance Scaled Messaging 2 (PSM2) library

openbabel

3.0.0_gcc-9.4.0

Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas.

opencv

4.5.4_gcc-9.4.0

OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library.

openexr

2.3.0_gcc-9.4.0

OpenEXR Graphics Tools (high dynamic-range image file format)

openfoam-org

8_gcc-9.4.0

OpenFOAM is a GPL-opensource C++ CFD-toolbox. The openfoam.org release is managed by the OpenFOAM Foundation Ltd as a licensee of the OPENFOAM trademark. This offering is not approved or endorsed by OpenCFD Ltd, producer and distributor of the OpenFOAM software via www.openfoam.com, and owner of the OPENFOAM trademark.

openjdk

11.0.12_7_gcc-9.4.0
1.8.0_265-b01_gcc-9.4.0

The free and opensource java implementation

openjpeg

2.3.1_gcc-9.4.0
2.4.0_gcc-9.4.0

OpenJPEG is an open-source JPEG 2000 codec written in C language.

openlibm

0.7.5_gcc-9.4.0

OpenLibm is an effort to have a high quality, portable, standalone C mathematical library

openmpi

4.1.2_gcc-9.4.0
4.1.2_intel-2021.5.0

An open source Message Passing Interface implementation.

openscenegraph

3.6.5_gcc-9.4.0

OpenSceneGraph is an open source, high performance 3D graphics toolkit that's used in a variety of visual simulation applications.

openssh

8.8p1_gcc-9.4.0
8.8p1_intel-2021.5.0

OpenSSH is the premier connectivity tool for remote login with the SSH protocol. It encrypts all traffic to eliminate eavesdropping, connection hijacking, and other attacks. In addition, OpenSSH provides a large suite of secure tunneling capabilities, several authentication methods, and sophisticated configuration options.

openssl

1.1.1m_gcc-9.4.0
1.1.1m_intel-2021.5.0

OpenSSL is an open source project that provides a robust, commercial-grade, and full-featured toolkit for the Transport Layer Security (TLS) and Secure Sockets Layer (SSL) protocols. It is also a general-purpose cryptography library.

opium

4.1_gcc-9.4.0

DFT pseudopotential generation project

opus

1.3.1_gcc-9.4.0

Opus is a totally open, royalty-free, highly versatile audio codec.

oracle-instant-client

21.1.0.0.0_gcc-9.4.0

Oracle instant client

osi

0.108.6_gcc-9.4.0

Osi (Open Solver Interface) provides an abstract base class to a generic linear programming (LP) solver, along with derived classes for specific solvers. Many applications may be able to use the Osi to insulate themselves from a specific LP solver. That is, programs written to the OSI standard may be linked to any solver with an OSI interface and should produce correct results. The OSI has been significantly extended compared to its first incarnation. Currently, the OSI supports linear programming solvers and has rudimentary support for integer programming.

p7zip

16.02_gcc-9.4.0

A Unix port of the 7z file archiver

pandoc

2.14.0.3_gcc-9.4.0

If you need to convert files from one markup format into another, pandoc is your swiss-army knife.

pango

1.42.0_gcc-9.4.0

Pango is a library for laying out and rendering of text, with an emphasis on internationalization. It 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.

papi

6.0.0.1_gcc-9.4.0

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 opportunities across the hardware and software stack.

parallel-netcdf

1.12.2_gcc-9.4.0
1.12.2_intel-2021.5.0

PnetCDF (Parallel netCDF) is a high-performance parallel I/O library for accessing files in format compatibility with Unidata's NetCDF, specifically the formats of CDF-1, 2, and 5.

parmetis

4.0.3_gcc-9.4.0
4.0.3_intel-2021.5.0

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.

patchelf

0.14.1_gcc-9.4.0

PatchELF is a small utility to modify the dynamic linker and RPATH of ELF executables.

pcre

8.45_gcc-9.4.0

The PCRE package contains Perl Compatible Regular Expression libraries. These are useful for implementing regular expression pattern matching using the same syntax and semantics as Perl 5.

pcre2

10.39_gcc-9.4.0

The PCRE2 package contains Perl Compatible Regular Expression libraries. These are useful for implementing regular expression pattern matching using the same syntax and semantics as Perl 5.

perl

5.34.0_gcc-9.4.0

Perl 5 is a highly capable, feature-rich programming language with over 27 years of development.

perl-acme-damn

0.08_gcc-9.4.0

Acme:Damn provides a single routine, damn(), which takes a blessed reference (a Perl object), and unblesses it, to return the original reference.

perl-algorithm-diff

1.1903_gcc-9.4.0

Compute 'intelligent' differences between two files / lists

perl-alien-build

1.86_gcc-9.4.0

This module provides tools for building external (non-CPAN) dependencies for CPAN. It is mainly designed to be used at install time of a CPAN client, and work closely with Alien:Base which is used at runtime.

perl-alien-libxml2

0.10_01_gcc-9.4.0

This module provides libxml2 for other modules to use.

perl-bioperl

1.7.6_gcc-9.4.0

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. These objects not only do what they are advertised to do in the documentation, but they also interact - Alignment objects are made from the Sequence objects, Sequence objects have access to Annotation and SeqFeature objects and databases, Blast objects can be converted to Alignment objects, and so on. This means that the objects provide a coordinated and extensible framework to do computational biology.

perl-bit-vector

7.4_gcc-9.4.0

Efficient bit vector, set of integers and 'big int' math library

perl-capture-tiny

0.46_gcc-9.4.0

Capture STDOUT and STDERR from Perl, XS or external programs

perl-carp-clan

6.06_gcc-9.4.0

Report errors from perspective of caller of a 'clan' of modules

perl-cgi

4.53_gcc-9.4.0

CGI - Handle Common Gateway Interface requests and responses

perl-class-data-inheritable

0.08_gcc-9.4.0

For creating accessor/mutators to class data.

perl-clone-choose

0.010_gcc-9.4.0

Checks several different modules which provides a clone() function and selects an appropriate one.

perl-data-dumper

2.173_gcc-9.4.0

Stringified perl data structures, suitable for both printing and eval

perl-data-stag

0.14_gcc-9.4.0

Structured Tags datastructures

perl-dbd-mysql

4.043_gcc-9.4.0

MySQL driver for the Perl5 Database Interface (DBI)

perl-dbd-pg

3.10.0_gcc-9.4.0

DBD:Pg is a Perl module that works with the DBI module to provide access to PostgreSQL databases.

perl-dbd-sqlite

1.59_01_gcc-9.4.0

DBD:SQLite - Self-contained RDBMS in a DBI Driver

perl-db-file

1.840_gcc-9.4.0

DB_File is a module which allows Perl programs to make use of the facilities provided by Berkeley DB version 1.x (if you have a newer version of DB, see 'Using DB_File with Berkeley DB version 2 or greater'). It is assumed that you have a copy of the Berkeley DB manual pages at hand when reading this documentation. The interface defined here mirrors the Berkeley DB interface closely.

perl-dbi

1.636_gcc-9.4.0

The DBI is the standard database interface module for Perl. It defines a set of methods, variables and conventions that provide a consistent database interface independent of the actual database being used.

perl-devel-stacktrace

2.02_gcc-9.4.0

An object representing a stack trace.

perl-devel-symdump

2.0604_gcc-9.4.0

Devel:Symdump - dump symbol names or the symbol table

perl-encode-locale

1.05_gcc-9.4.0

Determine the locale encoding

perl-error

0.17028_gcc-9.4.0

The Error package provides two interfaces. Firstly Error provides a procedural interface to exception handling. Secondly Error is a base class for errors/exceptions that can either be thrown, for subsequent catch, or can simply be recorded.

perl-exception-class

1.43_gcc-9.4.0

A module that allows you to declare real exception classes in Perl

perl-exporter-tiny

1.000000_gcc-9.4.0

An exporter with the features of Sub:Exporter but only core dependencies

perl-extutils-config

0.008_gcc-9.4.0

ExtUtils:Config - A wrapper for perl's configuration

perl-extutils-helpers

0.026_gcc-9.4.0

ExtUtils:Helpers - Various portability utilities for module builders

perl-extutils-installpaths

0.012_gcc-9.4.0

ExtUtils:InstallPaths - Build.PL install path logic made easy

perl-extutils-makemaker

7.24_gcc-9.4.0

ExtUtils:MakeMaker - Create a module Makefile. This utility is designed to write a Makefile for an extension module from a Makefile.PL. It is based on the Makefile.SH model provided by Andy Dougherty and the perl5-porters.

perl-ffi-checklib

0.25_gcc-9.4.0

This module checks whether a particular dynamic library is available for FFI to use. It is modeled heavily on Devel:CheckLib, but will find dynamic libraries even when development packages are not installed. It also provides a find_lib function that will return the full path to the found dynamic library, which can be feed directly into FFI::Platypus or another FFI system.

perl-file-chdir

0.1011_gcc-9.4.0

Perl's chdir() has the unfortunate problem of being very, very, very global. If any part of your program calls chdir() or if any library you use calls chdir(), it changes the current working directory for the whole program.

perl-file-copy-recursive

0.40_gcc-9.4.0

Perl extension for recursively copying files and directories

perl-file-homedir

1.004_gcc-9.4.0

Find your home and other directories on any platform

perl-file-listing

6.04_gcc-9.4.0

Parse directory listing

perl-file-sharedir-install

0.11_gcc-9.4.0

Install shared files

perl-file-which

1.22_gcc-9.4.0

Perl implementation of the which utility as an API

perl-forks

0.36_gcc-9.4.0

The 'forks' pragma allows a developer to use threads without having to have a threaded perl, or to even run 5.8.0 or higher.

perl-graph

0.9704_gcc-9.4.0

Graph data structures and algorithms

perl-hash-merge

0.300_gcc-9.4.0

Hash:Merge merges two arbitrarily deep hashes into a single hash.

perl-html-parser

3.72_gcc-9.4.0

HTML parser class

perl-html-tagset

3.20_gcc-9.4.0

Data tables useful in parsing HTML

perl-http-cookies

6.04_gcc-9.4.0

HTTP cookie jars

perl-http-daemon

6.01_gcc-9.4.0

A simple http server class

perl-http-date

6.02_gcc-9.4.0

Date conversion routines

perl-http-message

6.13_gcc-9.4.0

HTTP style message (base class)

perl-http-negotiate

6.01_gcc-9.4.0

Choose a variant to serve

perl-inline

0.80_gcc-9.4.0

Write Perl Subroutines in Other Programming Languages

perl-inline-c

0.78_gcc-9.4.0

C Language Support for Inline

perl-io-all

0.87_gcc-9.4.0

IO:All combines all of the best Perl IO modules into a single nifty object oriented interface to greatly simplify your everyday Perl IO idioms. It exports a single function called io, which returns a new IO::All object. And that object can do it all!

perl-io-html

1.001_gcc-9.4.0

Open an HTML file with automatic charset detection.

perl-io-prompt

0.997004_gcc-9.4.0

By default, this module exports a single function prompt. It prompts the user to enter some input, and returns an object that represents the user input.

perl-io-string

1.08_gcc-9.4.0

Emulate file interface for in-core strings

perl-io-stringy

2.111_gcc-9.4.0

This toolkit primarily provides modules for performing both traditional and object-oriented i/o) on things other than normal filehandles; in particular, IO:Scalar, IO::ScalarArray, and IO::Lines.

perl-io-tty

1.13_01_gcc-9.4.0

IO:Tty is used internally by IO::Pty to create a pseudo-tty. You wouldn't want to use it directly except to import constants, use IO::Pty. For a list of importable constants, see IO::Tty::Constant.

perl-ipc-run

20180523.0_gcc-9.4.0

IPC:Run allows you to run and interact with child processes using files, pipes, and pseudo-ttys. Both system()-style and scripted usages are supported and may be mixed. Likewise, functional and OO API styles are both supported and may be mixed.

perl-libwww-perl

6.33_gcc-9.4.0

The libwww-perl collection is a set of Perl modules which provides a simple and consistent application programming interface to the World-Wide Web. The main focus of the library is to provide classes and functions that allow you to write WWW clients.

perl-libxml-perl

0.08_gcc-9.4.0

libxml-perl is a collection of smaller Perl modules, scripts, and documents for working with XML in Perl. libxml-perl software works in combination with XML:Parser, PerlSAX, XML::DOM, XML::Grove and others.

perl-list-moreutils

0.428_gcc-9.4.0

Provide the stuff missing in List:Util

perl-list-moreutils-xs

0.428_gcc-9.4.0

List:MoreUtils::XS is a backend for List::MoreUtils. Even if it's possible (because of user wishes) to have it practically independent from List::MoreUtils, it technically depend on List::MoreUtils. Since it's only a backend, the API is not public and can change without any warning.

perl-logger-simple

2.0_gcc-9.4.0

Implementation of the Simran-Log-Log and Simran-Error-Error modules

perl-lwp-mediatypes

6.02_gcc-9.4.0

Guess media type for a file or a URL

perl-mailtools

2.21_gcc-9.4.0

Perl module for handling mail

perl-mce

1.874_gcc-9.4.0

MCE - Many-Core Engine for Perl providing parallel processing capabilities.

perl-module-build

0.4224_gcc-9.4.0

Module:Build is a system for building, testing, and installing Perl modules. It is meant to be an alternative to ExtUtils::MakeMaker. Developers may alter the behavior of the module through subclassing in a much more straightforward way than with MakeMaker. It also does not require a make on your system - most of the Module::Build code is pure-perl and written in a very cross-platform way.

perl-module-build-tiny

0.039_gcc-9.4.0

Module:Build::Tiny - A tiny replacement for Module::Build

perl-net-http

6.17_gcc-9.4.0

Low-level HTTP connection (client)

perl-object-insideout

4.05_gcc-9.4.0

Implements inside-out objects as anonymous scalar references that are blessed into a class with the scalar containing the ID for the object (usually a sequence number).

perl-parallel-forkmanager

1.19_gcc-9.4.0

A simple parallel processing fork manager

perl-parse-recdescent

1.967015_gcc-9.4.0

Generate Recursive-Descent Parsers

perl-path-tiny

0.108_gcc-9.4.0

This module provides a small, fast utility for working with file paths. It is friendlier to use than File:Spec and provides easy access to functions from several other core file handling modules. It aims to be smaller and faster than many alternatives on CPAN, while helping people do many common things in consistent and less error-prone ways.

perl-pegex

0.64_gcc-9.4.0

Acmeist PEG Parser Framework

perl-perl-unsafe-signals

0.03_gcc-9.4.0

Quoting perl581delta:

perl-readonly

2.05_gcc-9.4.0

Readonly - Facility for creating read-only scalars, arrays, hashes

perl-scalar-list-utils

1.50_gcc-9.4.0

Scalar:Util - A selection of general-utility scalar subroutines

perl-scalar-util-numeric

0.40_gcc-9.4.0

This module exports a number of wrappers around perl's builtin grok_number function, which returns the numeric type of its argument, or 0 if it isn't numeric.

perl-set-scalar

1.29_gcc-9.4.0

Set:Scalar - basic set operations

perl-sub-uplevel

0.2800_gcc-9.4.0

apparently run a function in a higher stack frame

perl-sys-sigaction

0.23_gcc-9.4.0

Prior to version 5.8.0 perl implemented 'unsafe' signal handling. The reason it is consider unsafe, is that there is a risk that a signal will arrive, and be handled while perl is changing internal data structures. This can result in all kinds of subtle and not so subtle problems. For this reason it has always been recommended that one do as little as possible in a signal handler, and only variables that already exist be manipulated.

perl-termreadkey

2.38_gcc-9.4.0

Term:ReadKey is a compiled perl module dedicated to providing simple control over terminal driver modes (cbreak, raw, cooked, etc.,) support for non-blocking reads, if the architecture allows, and some generalized handy functions for working with terminals. One of the main goals is to have the functions as portable as possible, so you can just plug in 'use Term::ReadKey' on any architecture and have a good likelihood of it working.

perl-test-deep

1.127_gcc-9.4.0

Extremely flexible deep comparison

perl-test-differences

0.64_gcc-9.4.0

Test strings and data structures and show differences if not ok

perl-test-exception

0.43_gcc-9.4.0

Test exception-based code

perl-test-most

0.35_gcc-9.4.0

Most commonly needed test functions and features.

perl-test-needs

0.002005_gcc-9.4.0

Skip tests when modules not available.

perl-test-requiresinternet

0.05_gcc-9.4.0

Easily test network connectivity

perl-test-warn

0.30_gcc-9.4.0

Perl extension to test methods for warnings

perl-text-diff

1.45_gcc-9.4.0

Provides a basic set of services akin to the GNU diff utility.

perl-text-soundex

3.05_gcc-9.4.0

Soundex is a phonetic algorithm for indexing names by sound, as pronounced in English. The goal is for names with the same pronunciation to be encoded to the same representation so that they can be matched despite minor differences in spelling

perl-thread-queue

3.13_gcc-9.4.0

Thread:Queue - Thread-safe queues.

perl-threads

2.21_gcc-9.4.0

threads - Perl interpreter-based threads

perl-timedate

2.30_gcc-9.4.0

The parser contained here will only parse absolute dates, if you want a date parser that can parse relative dates then take a look at the Time modules by David Muir on CPAN.

perl-try-tiny

0.28_gcc-9.4.0

Minimal try/catch with proper preservation of $@

perl-uri

1.72_gcc-9.4.0

Uniform Resource Identifiers (absolute and relative)

perl-want

0.29_gcc-9.4.0

A generalisation of wantarray.

perl-www-robotrules

6.02_gcc-9.4.0

Database of robots.txt-derived permissions

perl-xml-dom

1.46_gcc-9.4.0

This module extends the XML:Parser module by Clark Cooper. The XML::Parser module is built on top of XML::Parser::Expat, which is a lower level interface to James Clark's expat library.

perl-xml-dom-xpath

0.14_gcc-9.4.0

XML:DOM::XPath allows you to use XML::XPath methods to query a DOM. This is often much easier than relying only on getElementsByTagName.

perl-xml-filter-buffertext

1.01_gcc-9.4.0

This is a very simple filter. One common cause of grief (and programmer error) is that XML parsers aren't required to provide character events in one chunk. They can, but are not forced to, and most don't. This filter does the trivial but oft-repeated task of putting all characters into a single event.

perl-xml-libxml

2.0201_gcc-9.4.0

This module is an interface to libxml2, providing XML and HTML parsers with DOM, SAX and XMLReader interfaces, a large subset of DOM Layer 3 interface and a XML:XPath-like interface to XPath API of libxml2. The module is split into several packages which are not described in this section; unless stated otherwise, you only need to use XML::LibXML; in your programs.

perl-xml-namespacesupport

1.12_9_gcc-9.4.0

This module offers a simple to process namespaced XML names (unames) from within any application that may need them. It also helps maintain a prefix to namespace URI map, and provides a number of basic checks.

perl-xml-parser

2.44_gcc-9.4.0

XML:Parser - A perl module for parsing XML documents

perl-xml-quote

1.02_gcc-9.4.0

This module provides functions to quote/dequote strings in 'xml'-way.

perl-xml-regexp

0.04_gcc-9.4.0

This package contains regular expressions for the following XML tokens: BaseChar, Ideographic, Letter, Digit, Extender, CombiningChar, NameChar, EntityRef, CharRef, Reference, Name, NmToken, and AttValue.

perl-xml-sax

1.02_gcc-9.4.0

XML:SAX is a SAX parser access API for Perl. It includes classes and APIs required for implementing SAX drivers, along with a factory class for returning any SAX parser installed on the user's system.

perl-xml-sax-base

1.09_gcc-9.4.0

This module has a very simple task - to be a base class for PerlSAX drivers and filters. It's default behaviour is to pass the input directly to the output unchanged. It can be useful to use this module as a base class so you don't have to, for example, implement the characters() callback.

perl-xml-sax-writer

0.57_gcc-9.4.0

A new XML Writer was needed to match the SAX2 effort because quite naturally no existing writer understood SAX2. My first intention had been to start patching XML:Handler::YAWriter as it had previously been my favourite writer in the SAX1 world.

perl-xml-twig

3.52_gcc-9.4.0

This module provides a way to process XML documents. It is build on top of XML:Parser.

perl-xml-writer

0.625_gcc-9.4.0

XML:Writer is a helper module for Perl programs that write an XML document. The module handles all escaping for attribute values and character data and constructs different types of markup, such as tags, comments, and processing instructions.

perl-xml-xpathengine

0.14_gcc-9.4.0

This module provides an XPath engine, that can be re-used by other module/classes that implement trees.

perl-yaml

1.27_gcc-9.4.0

This module has been released to CPAN as YAML:Old, and soon YAML.pm will be changed to just be a frontend interface module for all the various Perl YAML implementation modules, including YAML::Old

perl-yaml-libyaml

0.67_gcc-9.4.0

Perl YAML Serialization using XS and libyaml

petsc

3.16.4_gcc-9.4.0
3.16.4_intel-2021.5.0

PETSc is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations.

pixman

0.40.0_gcc-9.4.0

The Pixman package contains a library that provides low-level pixel manipulation features such as image compositing and trapezoid rasterization.

pkgconf

1.8.0_gcc-9.4.0
1.8.0_intel-2021.5.0

pkgconf is a program which helps to configure compiler and linker flags for development frameworks. It is similar to pkg-config from freedesktop.org, providing additional functionality while also maintaining compatibility.

plumed

2.6.3_gcc-9.4.0

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.

poppler

0.79.0_gcc-9.4.0

Poppler is a PDF rendering library based on the xpdf-3.0 code base.

poppler-data

0.4.9_gcc-9.4.0

This package consists of encoding files for use with poppler. The encoding files are optional and poppler will automatically read them if they are present. When installed, the encoding files enables poppler to correctly render CJK and Cyrrilic properly. While poppler is licensed under the GPL, these encoding files have different license, and thus distributed separately.

popt

1.16_gcc-9.4.0

The popt library parses command line options.

postgresql

12.2_gcc-9.4.0
14.0_gcc-9.4.0

PostgreSQL is a powerful, open source object-relational database system. It has more than 15 years of active development and a proven architecture that has earned it a strong reputation for reliability, data integrity, and correctness.

proj

5.2.0_gcc-9.4.0
7.2.1_gcc-9.4.0
8.1.0_gcc-9.4.0

PROJ is a generic coordinate transformation software, that transforms geospatial coordinates from one coordinate reference system (CRS) to another. This includes cartographic projections as well as geodetic transformations.

protobuf

3.17.3_gcc-9.4.0
3.18.0_gcc-9.4.0

Google's data interchange format.

psimd

2020-05-17_gcc-9.4.0

Portable 128-bit SIMD intrinsics.

pthreadpool

2021-04-13_gcc-9.4.0

pthreadpool is a portable and efficient thread pool implementation.

py-absl-py

0.13.0_gcc-9.4.0

This repository is a collection of Python library code for building Python applications.

py-agate

1.6.1_gcc-9.4.0

agate is a Python data analysis library that is optimized for humans instead of machines. It is an alternative to numpy and pandas that solves real-world problems with readable code.

py-agate-dbf

0.2.1_gcc-9.4.0

agate-dbf adds read support for dbf files to agate.

py-agate-excel

0.2.3_gcc-9.4.0

agate-excel adds read support for Excel files (xls and xlsx) to agate.

py-agate-sql

0.5.4_gcc-9.4.0

agate-sql adds SQL read/write support to agate.

py-aiobotocore

1.2.1_gcc-9.4.0

Async client for amazon services using botocore and aiohttp/asyncio.

py-aiohttp

3.8.1_gcc-9.4.0

Supports both client and server side of HTTP protocol. Supports both client and server Web-Sockets out-of-the-box and avoids Callbacks. Provides Web-server with middlewares and plugable routing.

py-aioitertools

0.7.1_gcc-9.4.0

Implementation of itertools, builtins, and more for AsyncIO and mixed-type iterables.

py-aiosignal

1.2.0_gcc-9.4.0

A project to manage callbacks in asyncio projects.

py-alabaster

0.7.12_gcc-9.4.0

Alabaster is a visually (c)lean, responsive, configurable theme for the Sphinx documentation system.

py-anyio

3.5.0_gcc-9.4.0

High level compatibility layer for multiple asynchronous event loop implementations.

py-appdirs

1.4.4_gcc-9.4.0

A small Python module for determining appropriate platform-specific dirs, e.g. a 'user data dir'.

py-argon2-cffi

21.3.0_gcc-9.4.0

The secure Argon2 password hashing algorithm..

py-argon2-cffi-bindings

21.2.0_gcc-9.4.0

Low-level CFFI bindings for Argon2.

py-arm-pyart

1.12.7_gcc-9.4.0

Python ARM Radar Toolkit.

py-arviz

0.6.1_gcc-9.4.0

ArviZ (pronounced 'AR-vees') is a Python package for exploratory analysis of Bayesian models. Includes functions for posterior analysis, model checking, comparison and diagnostics.

py-ase

3.21.1_gcc-9.4.0

The Atomic Simulation Environment (ASE) is a set of tools and Python modules for setting up, manipulating, running, visualizing and analyzing atomistic simulations.

py-asttokens

2.0.5_gcc-9.4.0

Annotate AST trees with source code positions.

py-astunparse

1.6.3_gcc-9.4.0

An AST unparser for Python.

py-async-timeout

4.0.2_gcc-9.4.0

asyncio-compatible timeout context manager.

py-attrs

21.4.0_gcc-9.4.0

Classes Without Boilerplate

py-audioread

2.1.8_gcc-9.4.0

cross-library (GStreamer + Core Audio + MAD + FFmpeg) audio decoding for Python.

py-automat

20.2.0_gcc-9.4.0

Self-service finite-state machines for the programmer on the go.

py-auxlib

0.0.43_gcc-9.4.0

Auxlib is an auxiliary library to the python standard library.

py-awkward0

0.15.5_gcc-9.4.0

Manipulate arrays of complex data structures as easily as Numpy.

py-babel

2.9.1_gcc-9.4.0

Babel is an integrated collection of utilities that assist in internationalizing and localizing Python applications, with an emphasis on web-based applications.

py-backcall

0.2.0_gcc-9.4.0

Specifications for callback functions passed in to an API

py-backports-entry-points-selectable

1.1.1_gcc-9.4.0

Compatibility shim providing selectable entry points for older implementations

py-backports-weakref

1.0.post1_gcc-9.4.0

Backports of new features in Python's weakref module

py-beautifulsoup4

4.10.0_gcc-9.4.0

Beautiful Soup is a Python library for pulling data out of HTML and XML files. It works with your favorite parser to provide idiomatic ways of navigating, searching, and modifying the parse tree.

py-beniget

0.4.1_gcc-9.4.0

Extract semantic information about static Python code.

py-biopython

1.78_gcc-9.4.0

A distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics.

py-bitarray

0.8.1_gcc-9.4.0

Efficient array of booleans - C extension

py-black

22.1.0_gcc-9.4.0

Black is the uncompromising Python code formatter. By using it, you agree to cede control over minutiae of hand-formatting. In return, Black gives you speed, determinism, and freedom from pycodestyle nagging about formatting.

py-bleach

4.1.0_gcc-9.4.0

An easy allowlist-based HTML-sanitizing tool.

py-blinker

1.4_gcc-9.4.0

Fast, simple object-to-object and broadcast signaling

py-boto3

1.18.12_gcc-9.4.0

The AWS SDK for Python.

py-botocore

1.19.52_gcc-9.4.0
1.21.12_gcc-9.4.0

Low-level, data-driven core of boto 3.

py-bottleneck

1.3.2_gcc-9.4.0

A collection of fast NumPy array functions written in Cython.

py-bx-python

0.8.8_gcc-9.4.0

The bx-python project is a python library and associated set of scripts to allow for rapid implementation of genome scale analyses.

py-cachetools

4.2.4_gcc-9.4.0

This module provides various memoizing collections and decorators, including variants of the Python 3 Standard Library @lru_cache function decorator.

py-cartopy

0.18.0_gcc-9.4.0

Cartopy - a cartographic python library with matplotlib support.

py-certifi

2021.10.8_gcc-9.4.0

Certifi: A carefully curated collection of Root Certificates for validating the trustworthiness of SSL certificates while verifying the identity of TLS hosts.

py-cffi

1.15.0_gcc-9.4.0

Foreign Function Interface for Python calling C code

py-cftime

1.0.3.4_gcc-9.4.0

Python library for decoding time units and variable values in a netCDF file conforming to the Climate and Forecasting (CF) netCDF conventions

py-charset-normalizer

2.0.12_gcc-9.4.0

The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet.

py-click

8.0.3_gcc-9.4.0

Python composable command line interface toolkit.

py-colorama

0.4.4_gcc-9.4.0

Cross-platform colored terminal text.

py-colored

1.4.2_gcc-9.4.0

Simple library for color and formatting to terminal

py-configargparse

1.2.3_gcc-9.4.0

Applications with more than a handful of user-settable options are best configured through a combination of command line args, config files, hard-coded defaults, and in some cases, environment variables.

py-connectionpool

0.0.3_gcc-9.4.0

Thread-safe connection pool for python.

py-constantly

15.1.0_gcc-9.4.0

Symbolic constants in Python

py-cppy

1.1.0_gcc-9.4.0

C++ headers for C extension development

py-cryptography

36.0.1_gcc-9.4.0

cryptography is a package which provides cryptographic recipes and primitives to Python developers

py-csvkit

1.0.4_gcc-9.4.0

A library of utilities for working with CSV, the king of tabular file formats

py-cutadapt

2.10_gcc-9.4.0

Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.

py-cycler

0.11.0_gcc-9.4.0

Composable style cycles.

py-cylp

0.91.5_gcc-9.4.0

A Python interface for CLP, CBC, and CGL.

py-cython

0.29.24_gcc-9.4.0
3.0.0a9_gcc-9.4.0

The Cython compiler for writing C extensions for the Python language.

py-datrie

0.8.2_gcc-9.4.0

Super-fast, efficiently stored Trie for Python (2.x and 3.x). Uses libdatrie.

py-dbfread

2.0.7_gcc-9.4.0

DBF is a file format used by databases such dBase, Visual FoxPro, and FoxBase+. This library reads DBF files and returns the data as native Python data types for further processing. It is primarily intended for batch jobs and one-off scripts.

py-debugpy

1.5.1_gcc-9.4.0

An implementation of the Debug Adapter Protocol for Python.

py-decorator

4.4.2_gcc-9.4.0
5.1.1_gcc-9.4.0

The aim of the decorator module it to simplify the usage of decorators for the average programmer, and to popularize decorators by showing various non-trivial examples.

py-defusedxml

0.7.1_gcc-9.4.0

defusing XML bombs and other exploits

py-deprecation

2.1.0_gcc-9.4.0

The deprecation library provides a deprecated decorator and a fail_if_not_removed decorator for your tests.

py-distlib

0.3.4_gcc-9.4.0

Distribution utilities

py-distro

1.6.0_gcc-9.4.0

Distro - an OS platform information API.

py-dnaio

0.4.2_gcc-9.4.0

Read and write FASTQ and FASTA

py-docopt

0.6.2_gcc-9.4.0

Command-line interface description language.

py-docutils

0.17.1_gcc-9.4.0
0.18.1_gcc-9.4.0

Docutils is an open-source text processing system for processing plaintext documentation into useful formats, such as HTML, LaTeX, man-pages, open-document or XML. It includes reStructuredText, the easy to read, easy to use, what-you-see-is-what-you-get plaintext markup language.

py-entrypoints

0.4_gcc-9.4.0

Discover and load entry points from installed packages.

py-et-xmlfile

1.0.1_gcc-9.4.0

An implementation of lxml.xmlfile for the standard library.

py-executing

0.8.2_gcc-9.4.0

Get the currently executing AST node of a frame, and other information.

py-filelock

3.5.0_gcc-9.4.0

A platform-independent file lock for Python.

py-fisher

0.1.9_gcc-9.4.0

Fisher's Exact Test.

py-flask

2.0.2_gcc-9.4.0

A simple framework for building complex web applications.

py-flit

3.6.0_gcc-9.4.0

Flit is a simple way to put Python packages and modules on PyPI.

py-flit-core

3.2.0_gcc-9.4.0
3.6.0_gcc-9.4.0

Distribution-building parts of Flit.

py-fonttools

4.29.1_gcc-9.4.0

fontTools is a library for manipulating fonts, written in Python.

py-frozenlist

1.2.0_gcc-9.4.0

A list-like structure which implements collections.abc.MutableSequence.

py-fsspec

2021.7.0_gcc-9.4.0

A specification for pythonic filesystems.

py-future

0.18.2_gcc-9.4.0

Clean single-source support for Python 3 and 2

py-gast

0.4.0_gcc-9.4.0
0.5.3_gcc-9.4.0

Python AST that abstracts the underlying Python version

py-gevent

21.12.0_gcc-9.4.0

gevent is a coroutine-based Python networking library.

py-gitdb

4.0.9_gcc-9.4.0

The GitDB project implements interfaces to allow read and write access to git repositories.

py-gitpython

3.1.24_gcc-9.4.0

GitPython is a python library used to interact with Git repositories.

py-google-auth

2.3.2_gcc-9.4.0

This library simplifies using Google's various server-to-server authentication mechanisms to access Google APIs.

py-google-auth-oauthlib

0.4.6_gcc-9.4.0

This library provides oauthlib integration with google-auth.

py-googledrivedownloader

0.4_gcc-9.4.0

Minimal class to download shared files from Google Drive.

py-google-pasta

0.2.0_gcc-9.4.0

pasta is an AST-based Python refactoring library.

py-gpytorch

1.2.1_gcc-9.4.0

GPyTorch is a Gaussian process library implemented using PyTorch. GPyTorch is designed for creating scalable, flexible, and modular Gaussian process models with ease.

py-graphviz

0.13.2_gcc-9.4.0

Simple Python interface for Graphviz

py-greenlet

1.1.2_gcc-9.4.0

Lightweight in-process concurrent programming

py-grpcio

1.43.0_gcc-9.4.0

HTTP/2-based RPC framework.

py-h5py

3.6.0_gcc-9.4.0
3.6.0_gcc-9.4.0-mpi

The h5py package provides both a high- and low-level interface to the HDF5 library from Python.

py-html5lib

1.1_gcc-9.4.0

HTML parser based on the WHATWG HTML specification.

py-htseq

0.11.2_gcc-9.4.0

HTSeq is a Python package that provides infrastructure to process data from high-throughput sequencing assays.

py-hyperlink

21.0.0_gcc-9.4.0

A featureful, immutable, and correct URL for Python.

py-hypothesis

6.23.1_gcc-9.4.0

A library for property based testing.

py-idna

3.3_gcc-9.4.0

Internationalized Domain Names for Python (IDNA 2008 and UTS #46)

py-imageio

2.16.0_gcc-9.4.0

Python library for reading and writing image data.

py-imageio-ffmpeg

0.4.5_gcc-9.4.0

The purpose of this project is to provide a simple and reliable ffmpeg wrapper for working with video files. It implements two simple generator functions for reading and writing data from/to ffmpeg, which reliably terminate the ffmpeg process when done. It also takes care of publishing platform-specific wheels that include the binary ffmpeg executables.

py-imagesize

1.3.0_gcc-9.4.0

Parses image file headers and returns image size. Supports PNG, JPEG, JPEG2000, and GIF image file formats.

py-importlib-metadata

4.11.1_gcc-9.4.0

Read metadata from Python packages.

py-incremental

21.3.0_gcc-9.4.0

A small library that versions your Python projects.

py-iniconfig

1.1.1_gcc-9.4.0

iniconfig: brain-dead simple parsing of ini files

py-ipykernel

6.9.1_gcc-9.4.0

IPython Kernel for Jupyter

py-ipython

8.0.1_gcc-9.4.0

IPython provides a rich toolkit to help you make the most out of using Python interactively.

py-ipython-genutils

0.2.0_gcc-9.4.0

Vestigial utilities from IPython

py-ipywidgets

7.6.5_gcc-9.4.0

IPython widgets for the Jupyter Notebook

py-isodate

0.6.1_gcc-9.4.0

This module implements ISO 8601 date, time and duration parsing. The implementation follows ISO8601:2004 standard, and implements only date/time representations mentioned in the standard. If something is not mentioned there, then it is treated as non existent, and not as an allowed option.

py-itk

5.1.2-cp39_gcc-9.4.0

ITK is an open-source toolkit for multidimensional image analysis

py-itsdangerous

2.0.1_gcc-9.4.0

Various helpers to pass trusted data to untrusted environments.

py-jdcal

1.3_gcc-9.4.0

Julian dates from proleptic Gregorian and Julian calendars

py-jedi

0.18.1_gcc-9.4.0

An autocompletion tool for Python that can be used for text editors.

py-jinja2

3.0.3_gcc-9.4.0

Jinja2 is a template engine written in pure Python. It provides a Django inspired non-XML syntax but supports inline expressions and an optional sandboxed environment.

py-jmespath

0.10.0_gcc-9.4.0

JSON Matching Expressions.

py-joblib

1.1.0_gcc-9.4.0

Lightweight pipelining with Python functions.

py-json5

0.9.6_gcc-9.4.0

The JSON5 Data Interchange Format (JSON5) is a superset of JSON that aims to alleviate some of the limitations of JSON by expanding its syntax to include some productions from ECMAScript 5.1.

py-jsonschema

4.4.0_gcc-9.4.0

Jsonschema: An(other) implementation of JSON Schema for Python.

py-jupyter

1.0.0_gcc-9.4.0

Jupyter metapackage. Install all the Jupyter components in one go.

py-jupyter-client

7.1.2_gcc-9.4.0

Jupyter protocol client APIs

py-jupyter-console

6.4.0_gcc-9.4.0

Jupyter Terminal Console

py-jupyter-core

4.9.2_gcc-9.4.0

Core Jupyter functionality

py-jupyterlab

3.2.9_gcc-9.4.0

JupyterLab is the next-generation web-based user interface for Project Jupyter.

py-jupyterlab-pygments

0.1.2_gcc-9.4.0

Pygments theme using JupyterLab CSS variables.

py-jupyterlab-server

2.10.3_gcc-9.4.0

A set of server components for JupyterLab and JupyterLab like applications

py-jupyterlab-widgets

1.0.2_gcc-9.4.0

A JupyterLab extension.

py-jupyter-packaging11

0.11.1_gcc-9.4.0

Jupyter Packaging Utilities, version 11.

py-jupyter-packaging7

0.7.12_gcc-9.4.0

Jupyter Packaging Utilities, version 7.

py-jupyter-server

1.13.5_gcc-9.4.0

The Jupyter Server provides the backend (i.e. the core services, APIs, and REST endpoints) for Jupyter web applications like Jupyter notebook, JupyterLab, and Voila.

py-keras

2.7.0_gcc-9.4.0

Deep Learning library for Python. Convnets, recurrent neural networks, and more. Runs on Theano or TensorFlow.

py-keras-preprocessing

1.1.2_gcc-9.4.0

Utilities for working with image data, text data, and sequence data.

py-kiwisolver

1.3.2_gcc-9.4.0

A fast implementation of the Cassowary constraint solver

py-leather

0.3.3_gcc-9.4.0

Leather is the Python charting library for those who need charts now and don't care if they're perfect.

py-libclang

11.1.0_gcc-9.4.0

The repository contains code that taken from the LLVM project, to make it easier to install clang's python bindings.

py-librosa

0.7.2_gcc-9.4.0

A python package for music and audio analysis.

py-llvmlite

0.38.0_gcc-9.4.0

A lightweight LLVM python binding for writing JIT compilers

py-lz4

3.1.3_gcc-9.4.0

lz4 (compression library) bindings for Python

py-m2r

0.2.1_gcc-9.4.0

M2R converts a markdown file including reStructuredText (rst) markups to a valid rst format.

py-mako

1.1.6_gcc-9.4.0

A super-fast templating language that borrows the best ideas from the existing templating languages.

py-markdown

3.3.4_gcc-9.4.0

This is a Python implementation of John Gruber's Markdown. It is almost completely compliant with the reference implementation, though there are a few very minor differences. See John's Syntax Documentation for the syntax rules.

py-markupsafe

2.0.1_gcc-9.4.0

MarkupSafe is a library for Python that implements a unicode string that is aware of HTML escaping rules and can be used to implement automatic string escaping. It is used by Jinja 2, the Mako templating engine, the Pylons web framework and many more.

py-matplotlib

3.5.1_gcc-9.4.0

Matplotlib is a comprehensive library for creating static, animated, and interactive visualizations in Python.

py-matplotlib-inline

0.1.3_gcc-9.4.0

Inline Matplotlib backend for Jupyter.

py-misopy

0.5.4_gcc-9.4.0

MISO (Mixture of Isoforms) is a probabilistic framework that quantitates the expression level of alternatively spliced genes from RNA-Seq data, and identifies differentially regulated isoforms or exons across samples.

py-mistune

0.8.4_gcc-9.4.0

A sane Markdown parser with useful plugins and renderers.

py-mock

4.0.3_gcc-9.4.0

mock is a library for testing in Python. It allows you to replace parts of your system under test with mock objects and make assertions about how they have been used.

py-moviepy

1.0.3_gcc-9.4.0

MoviePy is a Python module for video editing, which can be used for basic operations (like cuts, concatenations, title insertions), video compositing (a.k.a. non-linear editing), video processing, or to create advanced effects. It can read and write the most common video formats, including GIF.

py-mpi4py

3.1.2_gcc-9.4.0

This package provides Python bindings for the Message Passing Interface (MPI) standard. It is implemented on top of the MPI-1/MPI-2 specification and exposes an API which grounds on the standard MPI-2 C++ bindings.

py-mpmath

1.2.1_gcc-9.4.0

A Python library for arbitrary-precision floating-point arithmetic.

py-multidict

6.0.2_gcc-9.4.0

Multidict is dict-like collection of key-value pairs where key might be occurred more than once in the container.

py-mypy-extensions

0.4.3_gcc-9.4.0

Experimental type system extensions for programs checked with the mypy typechecker.

py-nbclassic

0.3.5_gcc-9.4.0

Jupyter Notebook as a Jupyter Server Extension.

py-nbclient

0.5.5_gcc-9.4.0

A client library for executing notebooks.

py-nbconvert

6.4.2_gcc-9.4.0

Jupyter Notebook Conversion

py-nbformat

5.1.3_gcc-9.4.0

The Jupyter Notebook format

py-nest-asyncio

1.5.4_gcc-9.4.0

Patch asyncio to allow nested event loops.

py-netcdf4

1.5.3_gcc-9.4.0

Python interface to the netCDF Library.

py-networkx

2.6.3_gcc-9.4.0

NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks.

py-notebook

6.4.5_gcc-9.4.0

Jupyter Interactive Notebook

py-numba

0.55.1_gcc-9.4.0

NumPy aware dynamic Python compiler using LLVM

py-numexpr

2.7.3_gcc-9.4.0

Fast numerical expression evaluator for NumPy

py-numpy

1.21.5_gcc-9.4.0

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, and useful linear algebra, Fourier transform, and random number capabilities

py-numpydoc

1.1.0_gcc-9.4.0

numpydoc - Numpy's Sphinx extensions

py-oauthlib

3.1.0_gcc-9.4.0

A generic, spec-compliant, thorough implementation of the OAuth request-signing logic

py-openpyxl

3.0.3_gcc-9.4.0

A Python library to read/write Excel 2010 xlsx/xlsm files

py-opt-einsum

3.3.0_gcc-9.4.0

Optimized Einsum: A tensor contraction order optimizer.

py-ordereddict

1.1_gcc-9.4.0

A drop-in substitute for Py2.7's new collections. OrderedDict that works in Python 2.4-2.6.

py-packaging

21.3_gcc-9.4.0

Core utilities for Python packages.

py-pandas

1.4.1_gcc-9.4.0

pandas is a fast, powerful, flexible and easy to use open source data analysis and manipulation tool, built on top of the Python programming language.

py-pandocfilters

1.5.0_gcc-9.4.0

A python module for writing pandoc filters

py-parsedatetime

2.5_gcc-9.4.0

Parse human-readable date/time strings.

py-parso

0.8.2_gcc-9.4.0

Parso is a Python parser that supports error recovery and round-trip parsing for different Python versions (in multiple Python versions). Parso is also able to list multiple syntax errors in your python file.

py-pathspec

0.9.0_gcc-9.4.0

pathspec extends the test loading and running features of unittest, making it easier to write, find and run tests.

py-patsy

0.5.1_gcc-9.4.0

A Python package for describing statistical models and for building design matrices.

py-pexpect

4.8.0_gcc-9.4.0

Pexpect allows easy control of interactive console applications.

py-pickleshare

0.7.5_gcc-9.4.0

Tiny 'shelve'-like database with concurrency support

py-pillow

9.0.0_gcc-9.4.0

Pillow is a fork of the Python Imaging Library (PIL). It adds image processing capabilities to your Python interpreter. This library supports many file formats, and provides powerful image processing and graphics capabilities.

py-pip

21.3.1_gcc-9.4.0

The PyPA recommended tool for installing Python packages.

py-pkgconfig

1.5.5_gcc-9.4.0

Interface Python with pkg-config.

py-platformdirs

2.4.0_gcc-9.4.0

A small Python module for determining appropriate platform-specific dirs, e.g. a 'user data dir'

py-pluggy

1.0.0_gcc-9.4.0

Plugin and hook calling mechanisms for python.

py-ply

3.11_gcc-9.4.0

Python Lex & Yacc.

py-poetry-core

1.0.7_gcc-9.4.0

Poetry PEP 517 Build Backend.

py-pooch

1.5.2_gcc-9.4.0

Pooch manages your Python library's sample data files: it automatically downloads and stores them in a local directory, with support for versioning and corruption checks.

py-proglog

0.1.9_gcc-9.4.0

Proglog is a progress logging system for Python. It allows to build complex libraries while giving the user control on the management of logs, callbacks and progress bars.

py-prometheus-client

0.12.0_gcc-9.4.0

Prometheus instrumentation library for Python applications.

py-prompt-toolkit

3.0.24_gcc-9.4.0

Library for building powerful interactive command lines in Python

py-protobuf

3.17.3_gcc-9.4.0

Protocol buffers are Google's language-neutral, platform-neutral, extensible mechanism for serializing structured data - think XML, but smaller, faster, and simpler. You define how you want your data to be structured once, then you can use special generated source code to easily write and read your structured data to and from a variety of data streams and using a variety of languages.

py-psutil

5.8.0_gcc-9.4.0

psutil is a cross-platform library for retrieving information on running processes and system utilization (CPU, memory, disks, network) in Python.

py-psycopg2

2.9.1_gcc-9.4.0

Python interface to PostgreSQL databases

py-ptyprocess

0.7.0_gcc-9.4.0

Run a subprocess in a pseudo terminal

py-pulp

2.6.0_gcc-9.4.0

PuLP is an LP modeler written in Python. PuLP can generate MPS or LP files and call GLPK, COIN-OR CLP/CBC, CPLEX, GUROBI, MOSEK, XPRESS, CHOCO, MIPCL, SCIP to solve linear problems.

py-pure-eval

0.2.2_gcc-9.4.0

Safely evaluate AST nodes without side effects.

py-py

1.11.0_gcc-9.4.0

Library with cross-python path, ini-parsing, io, code, log facilities

py-pyasn1

0.4.8_gcc-9.4.0

Pure-Python implementation of ASN.1 types and DER/BER/CER codecs (X.208).

py-pyasn1-modules

0.2.8_gcc-9.4.0

A collection of ASN.1 modules expressed in form of pyasn1 classes. Includes protocols PDUs definition (SNMP, LDAP etc.) and various data structures (X.509, PKCS etc.).

py-pybigwig

0.3.12_gcc-9.4.0

A package for accessing bigWig files using libBigWig.

py-pybind11

2.6.2_gcc-9.4.0

pybind11 – Seamless operability between C++11 and Python.

py-pycifrw

4.4.1_gcc-9.4.0

Python library for interacting with Crystallographic Information Framework (CIF) files.

py-pycparser

2.20_gcc-9.4.0

A complete parser of the C language, written in pure python.

py-pydicom

2.1.2_gcc-9.4.0

Pure python package for DICOM medical file reading and writing

py-pydot

1.4.2_gcc-9.4.0

Python interface to Graphviz's Dot language

py-pygments

2.10.0_gcc-9.4.0

Pygments is a syntax highlighting package written in Python.

py-pygpu

0.7.6_gcc-9.4.0

Python packge for the libgpuarray C library.

py-pyjwt

2.1.0_gcc-9.4.0

JSON Web Token implementation in Python

py-pymc3

3.8_gcc-9.4.0

PyMC3 is a Python package for Bayesian statistical modeling and Probabilistic Machine Learning focusing on advanced Markov chain Monte Carlo (MCMC) and variational inference (VI) algorithms. Its flexibility and extensibility make it applicable to a large suite of problems.

py-pymysql

0.9.2_gcc-9.4.0

Pure-Python MySQL client library

py-pyparsing

3.0.6_gcc-9.4.0

A Python Parsing Module.

py-pyqt5

5.13.1_gcc-9.4.0

PyQt is a set of Python v2 and v3 bindings for The Qt Company's Qt application framework and runs on all platforms supported by Qt including Windows, OS X, Linux, iOS and Android. PyQt5 supports Qt v5.

py-pyrsistent

0.18.0_gcc-9.4.0

Pyrsistent is a number of persistent collections (by some referred to as functional data structures). Persistent in the sense that they are immutable.

py-pysam

0.18.0_gcc-9.4.0

A python module for reading, manipulating and writing genomic data sets.

py-pyshp

2.1.0_gcc-9.4.0

The Python Shapefile Library (pyshp) reads and writes ESRI Shapefiles in pure Python.

py-pytest

6.2.5_gcc-9.4.0

pytest: simple powerful testing with Python.

py-pytest-runner

5.3.1_gcc-9.4.0

Invoke py.test as distutils command with dependency resolution.

py-python-box

5.3.0_gcc-9.4.0

Advanced Python dictionaries with dot notation access

py-python-dateutil

2.8.2_gcc-9.4.0

Extensions to the standard Python datetime module.

py-python-louvain

0.15_gcc-9.4.0

This module implements community detection. It uses the louvain method described in Fast unfolding of communities in large networks, Vincent D Blondel, Jean-Loup Guillaume, Renaud Lambiotte, Renaud Lefebvre, Journal of Statistical Mechanics: Theory and Experiment 2008(10), P10008 (12pp)

py-python-slugify

4.0.0_gcc-9.4.0

A Python Slugify application that handles Unicode

py-pythran

0.10.0_gcc-9.4.0

Ahead of Time compiler for numeric kernels.

py-pytimeparse

1.1.8_gcc-9.4.0

A small Python library to parse various kinds of time expressions.

py-pytorch-gradual-warmup-lr

0.3.2_gcc-9.4.0

Gradually warm-up (increasing) learning rate for pytorch's optimizer.

py-pytz

2021.3_gcc-9.4.0

World timezone definitions, modern and historical.

py-pyvcf

0.6.8_gcc-9.4.0

A Variant Call Format reader for Python

py-pywavelets

1.1.1_gcc-9.4.0

PyWavelets is a free Open Source library for wavelet transforms in Python

py-pyyaml

6.0_gcc-9.4.0

PyYAML is a YAML parser and emitter for Python.

py-pyzmq

22.3.0_gcc-9.4.0

PyZMQ: Python bindings for zeromq.

py-qtconsole

5.2.0_gcc-9.4.0

Jupyter Qt console

py-qtpy

1.11.2_gcc-9.4.0

QtPy: Abtraction layer for PyQt5/PyQt4/PySide/PySide2

py-ratelimiter

1.2.0.post0_gcc-9.4.0

Simple Python module providing rate limiting.

py-rdflib

6.0.2_gcc-9.4.0

RDFLib is a pure Python package for working with RDF. RDFLib contains most things you need to work with RDF, including: parsers and serializers for RDF/XML, N3, NTriples, N-Quads, Turtle, TriX, Trig and JSON-LD (via a plugin). a Graph interface which can be backed by any one of a number of Store implementations store implementations for in-memory storage and persistent storage on top of the Berkeley DB a SPARQL 1.1 implementation - supporting SPARQL 1.1 Queries and Update statements

py-reindent

3.5.1_gcc-9.4.0

Change Python (.py) files to use 4-space indents and no hard tab characters. Also trim excess spaces and tabs from ends of lines, and remove empty lines at the end of files. Also ensure the last line ends with a newline.

py-reportlab

3.4.0_gcc-9.4.0

The ReportLab Toolkit. An Open Source Python library for generating PDFs and graphics.

py-requests

2.26.0_gcc-9.4.0

Python HTTP for Humans.

py-requests-oauthlib

1.3.0_gcc-9.4.0

This project provides first-class OAuth library support for Requests.

py-resampy

0.2.2_gcc-9.4.0

Efficient sample rate conversion in python

py-rpy2

3.0.4_gcc-9.4.0

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.

py-rsa

4.7.2_gcc-9.4.0

Pure-Python RSA implementation

py-rseqc

3.0.1_gcc-9.4.0

RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data.

py-rst2pdf

0.99_gcc-9.4.0

Convert reStructured Text to PDF via ReportLab.

py-ruamel-yaml

0.17.16_gcc-9.4.0

a YAML parser/emitter that supports roundtrip preservation of comments, seq/map flow style, and map key order

py-s3fs

0.5.2_gcc-9.4.0

S3FS builds on aiobotocore to provide a convenient Python filesystem interface for S3.

py-s3transfer

0.5.0_gcc-9.4.0

S3transfer is a Python library for managing Amazon S3 transfers.

py-scikit-build

0.12.0_gcc-9.4.0

scikit-build is an improved build system generator for CPython C/C++/Fortran/Cython extensions. It provides better support for additional compilers, build systems, cross compilation, and locating dependencies and their associated build requirements.

py-scikit-image

0.18.3_gcc-9.4.0

Image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.

py-scikit-learn

1.0.2_gcc-9.4.0

A set of python modules for machine learning and data mining.

py-scikit-learn-extra

0.2.0_gcc-9.4.0

A set of useful tools compatible with scikit-learn

py-scikit-optimize

0.5.2_gcc-9.4.0

Scikit-Optimize, or skopt, is a simple and efficient library to minimize (very) expensive and noisy black-box functions. It implements several methods for sequential model-based optimization. skopt aims to be accessible and easy to use in many contexts.

py-scipy

1.8.0_gcc-9.4.0

SciPy (pronounced 'Sigh Pie') is a Scientific Library for Python. It provides many user-friendly and efficient numerical routines such as routines for numerical integration and optimization.

py-semantic-version

2.8.2_gcc-9.4.0

This small python library provides a few tools to handle SemVer in Python. It follows strictly the 2.0.0 version of the SemVer scheme.

py-semver

2.8.1_gcc-9.4.0

A Python module for semantic versioning. Simplifies comparing versions.

py-send2trash

1.8.0_gcc-9.4.0

Python library to send files to Trash/Recycle on all platforms.

py-sentencepiece

0.1.91_gcc-9.4.0

Unsupervised text tokenizer for Neural Network-based text generation.

py-setuptools

57.4.0_gcc-9.4.0
59.4.0_gcc-9.4.0

A Python utility that aids in the process of downloading, building, upgrading, installing, and uninstalling Python packages.

py-setuptools-rust

0.12.1_gcc-9.4.0

Setuptools rust extension plugin.

py-setuptools-scm

6.3.2_gcc-9.4.0

The blessed package to manage your versions by scm tags.

py-setuptools-scm-git-archive

1.1_gcc-9.4.0

This is a setuptools_scm plugin that adds support for git archives (for example the ones GitHub automatically generates).

py-shapely

1.8.1_gcc-9.4.0

Manipulation and analysis of geometric objects in the Cartesian plane.

py-simplegeneric

0.8.1_gcc-9.4.0

Simple generic functions (similar to Python's own len(), pickle.dump(), etc.)

py-sip

4.19.21_gcc-9.4.0-qt5

A Python bindings generator for C/C++ libraries.

py-six

1.16.0_gcc-9.4.0

Python 2 and 3 compatibility utilities.

py-smart-open

5.2.1_gcc-9.4.0

smart_open is a Python 2 & Python 3 library for efficient streaming of very large files from/to S3, HDFS, WebHDFS, HTTP, or local storage. It supports transparent, on-the-fly (de-)compression for a variety of different formats.

py-smartypants

2.0.1_gcc-9.4.0

smartypants is a Python fork of SmartyPants.

py-smmap

3.0.4_gcc-9.4.0

A pure Python implementation of a sliding window memory map manager

py-sniffio

1.2.0_gcc-9.4.0

This is a tiny package whose only purpose is to let you detect which async library your code is running under.

py-snowballstemmer

2.0.0_gcc-9.4.0

This package provides 16 stemmer algorithms (15 + Poerter English stemmer) generated from Snowball algorithms.

py-sortedcontainers

2.1.0_gcc-9.4.0

Sorted Containers is an Apache2 licensed sorted collections library, written in pure-Python, and fast as C-extensions.

py-soundfile

0.10.3.post1_gcc-9.4.0

SoundFile is an audio library based on libsndfile, CFFI and NumPy.

py-soupsieve

2.2.1_gcc-9.4.0

A modern CSS selector implementation for Beautiful Soup.

py-sphinx

4.4.0_gcc-9.4.0

Sphinx Documentation Generator.

py-sphinxcontrib-applehelp

1.0.1_gcc-9.4.0

sphinxcontrib-applehelp is a sphinx extension which outputs Apple help books.

py-sphinxcontrib-devhelp

1.0.1_gcc-9.4.0

sphinxcontrib-devhelp is a sphinx extension which outputs Devhelp document.

py-sphinxcontrib-htmlhelp

2.0.0_gcc-9.4.0

sphinxcontrib-htmlhelp is a sphinx extension which outputs htmlhelp document.

py-sphinxcontrib-jsmath

1.0.1_gcc-9.4.0

A sphinx extension which renders display math in HTML via JavaScript.

py-sphinxcontrib-qthelp

1.0.2_gcc-9.4.0

sphinxcontrib-qthelp is a sphinx extension which outputs QtHelp document.

py-sphinxcontrib-serializinghtml

1.1.5_gcc-9.4.0

sphinxcontrib-serializinghtml is a sphinx extension which outputs 'serialized' HTML files (json and pickle).

py-sqlalchemy

1.4.20_gcc-9.4.0

The Python SQL Toolkit and Object Relational Mapper

py-stack-data

0.2.0_gcc-9.4.0

Extract data from python stack frames and tracebacks for informative displays.

py-stopit

1.1.2_gcc-9.4.0

Raise asynchronous exceptions in other threads, control the timeout of blocks or callables with two context managers and two decorators.

py-sympy

1.8_gcc-9.4.0

SymPy is a Python library for symbolic mathematics.

py-tables

3.6.1_gcc-9.4.0

PyTables is a package for managing hierarchical datasets and designed to efficiently and easily cope with extremely large amounts of data.

py-tabulate

0.8.9_gcc-9.4.0

Pretty-print tabular data

py-tensorboard

2.7.0_gcc-9.4.0

TensorBoard is a suite of web applications for inspecting and understanding your TensorFlow runs and graphs.

py-tensorboard-data-server

0.6.1_gcc-9.4.0

Fast data loading for TensorBoard

py-tensorboard-plugin-wit

1.8.1_gcc-9.4.0

The What-If Tool makes it easy to efficiently and intuitively explore up to two models' performance on a dataset. Investigate model performances for a range of features in your dataset, optimization strategies and even manipulations to individual datapoint values. All this and more, in a visual way that requires minimal code.

py-tensorflow

2.7.0_gcc-9.4.0

TensorFlow is an Open Source Software Library for Machine Intelligence

py-tensorflow-estimator

2.7.0_gcc-9.4.0

TensorFlow Estimator is a high-level TensorFlow API that greatly simplifies machine learning programming.

py-termcolor

1.1.0_gcc-9.4.0

ANSII Color formatting for output in terminal.

py-terminado

0.12.1_gcc-9.4.0

Terminals served to term.js using Tornado websockets

py-testpath

0.5.0_gcc-9.4.0

Testpath is a collection of utilities for Python code working with files and commands.

py-text-unidecode

1.3_gcc-9.4.0

text-unidecode is the most basic port of the Text:Unidecode Perl library.

py-theano

1.0.5_gcc-9.4.0

Optimizing compiler for evaluating mathematical expressions on CPUs and GPUs.

pythia8

8.306_gcc-9.4.0

The Pythia program is a standard tool for the generation of events in high-energy collisions, comprising a coherent set of physics models for the evolution from a few-body hard process to a complex multiparticle final state.

python

3.9.9_gcc-9.4.0

The Python programming language.

py-threadpoolctl

3.0.0_gcc-9.4.0

Python helpers to limit the number of threads used in the threadpool-backed of common native libraries used for scientific computing and data science (e.g. BLAS and OpenMP).

py-tifffile

2021.11.2_gcc-9.4.0

Read and write image data from and to TIFF files.

py-toml

0.10.2_gcc-9.4.0

A Python library for parsing and creating TOML configuration files. For more information on the TOML standard, see https://github.com/toml-lang/toml.git

py-tomli

1.2.2_gcc-9.4.0

Tomli is a Python library for parsing TOML.

py-tomli-w

1.0.0_gcc-9.4.0

A lil' TOML writer.

py-tomlkit

0.7.2_gcc-9.4.0

Style preserving TOML library

py-toposort

1.6_gcc-9.4.0

Implements a topological sort algorithm.

py-torch

1.10.2_gcc-9.4.0

Tensors and Dynamic neural networks in Python with strong GPU acceleration.

py-torchaudio

0.4.0_gcc-9.4.0

The aim of torchaudio is to apply PyTorch to the audio domain. By supporting PyTorch, torchaudio follows the same philosophy of providing strong GPU acceleration, having a focus on trainable features through the autograd system, and having consistent style (tensor names and dimension names). Therefore, it is primarily a machine learning library and not a general signal processing library. The benefits of Pytorch is be seen in torchaudio through having all the computations be through Pytorch operations which makes it easy to use and feel like a natural extension.

py-torch-cluster

1.5.8_gcc-9.4.0

This package consists of a small extension library of highly optimized graph cluster algorithms for the use in PyTorch.

py-torchfile

0.1.0_gcc-9.4.0

Mostly direct port of the torch7 Lua and C serialization implementation to Python, depending only on numpy (and the standard library: array and struct). Sharing of objects including torch.Tensors is preserved.

py-torch-geometric

1.6.3_gcc-9.4.0

PyTorch Geometric (PyG) is a geometric deep learning extension library for PyTorch. It consists of various methods for deep learning on graphs and other irregular structures, also known as geometric deep learning, from a variety of published papers. In addition, it consists of an easy-to-use mini-batch loader for many small and single giant graphs, multi gpu-support, a large number of common benchmark datasets (based on simple interfaces to create your own), and helpful transforms, both for learning on arbitrary graphs as well as on 3D meshes or point clouds.

py-torch-nvidia-apex

2020-10-19_gcc-9.4.0

A PyTorch Extension: Tools for easy mixed precision and distributed training in Pytorch

py-torch-scatter

2.0.5_gcc-9.4.0

This package consists of a small extension library of highly optimized sparse update (scatter and segment) operations for the use in PyTorch, which are missing in the main package.

py-torch-sparse

0.6.8_gcc-9.4.0

This package consists of a small extension library of optimized sparse matrix operations with autograd support.

py-torch-spline-conv

1.2.0_gcc-9.4.0

This is a PyTorch implementation of the spline-based convolution operator of SplineCNN.

py-torchsummary

1.5.1_gcc-9.4.0

Keras has a neat API to view the visualization of the model which is very helpful while debugging your network. Here is a barebone code to try and mimic the same in PyTorch. The aim is to provide information complementary to, what is not provided by print(your_model) in PyTorch.

py-torchtext

0.5.0_gcc-9.4.0

Text utilities and datasets for PyTorch.

py-torchvision

0.11.3_gcc-9.4.0

The torchvision package consists of popular datasets, model architectures, and common image transformations for computer vision.

py-tornado

6.1_gcc-9.4.0

Tornado is a Python web framework and asynchronous networking library.

py-tqdm

4.62.3_gcc-9.4.0

A Fast, Extensible Progress Meter

py-traitlets

5.1.1_gcc-9.4.0

Traitlets Python config system

py-twisted

21.7.0_gcc-9.4.0

An asynchronous networking framework written in Python

py-typing-extensions

3.10.0.2_gcc-9.4.0

The typing_extensions module contains both backports of these changes as well as experimental types that will eventually be added to the typing module, such as Protocol (see PEP 544 for details about protocols and static duck typing).

py-uproot3

3.14.4_gcc-9.4.0

ROOT I/O in pure Python and Numpy.

py-uproot3-methods

0.10.1_gcc-9.4.0

Pythonic mix-ins for ROOT classes.

py-urllib3

1.26.6_gcc-9.4.0

HTTP library with thread-safe connection pooling, file post, and more.

py-virtualenv

20.10.0_gcc-9.4.0

virtualenv is a tool to create isolated Python environments.

py-wcwidth

0.2.5_gcc-9.4.0

Measures number of Terminal column cells of wide-character codes

py-webencodings

0.5.1_gcc-9.4.0

This is a Python implementation of the WHATWG Encoding standard.

py-websocket-client

1.2.1_gcc-9.4.0

WebSocket client for Python. hybi13 is supported.

py-werkzeug

2.0.2_gcc-9.4.0

The Swiss Army knife of Python web development

py-wget

3.2_gcc-9.4.0

pure python download utility

py-wheel

0.37.0_gcc-9.4.0

A built-package format for Python.

py-widgetsnbextension

3.5.1_gcc-9.4.0

IPython HTML widgets for Jupyter

py-wradlib

1.5.0_gcc-9.4.0

wradlib is designed to assist you in the most important steps of processing weather radar data. These may include: reading common data formats, georeferencing, converting reflectivity to rainfall intensity, identifying and correcting typical error sources (such as clutter or attenuation) and visualising the data.

py-wrapt

1.13.3_gcc-9.4.0

Module for decorators, wrappers and monkey patching.

py-xarray

0.18.2_gcc-9.4.0

N-D labeled arrays and datasets in Python

py-xlrd

2.0.1_gcc-9.4.0

Library for developers to extract data from Microsoft Excel (tm) spreadsheet files

py-xmltodict

0.12.0_gcc-9.4.0

xmltodict is a Python module that makes working with XML feel like you are working with JSON.

py-xopen

0.8.4_gcc-9.4.0

This small Python module provides a xopen function that works like the built-in open function, but can also deal with compressed files. Supported compression formats are gzip, bzip2 and xz. They are automatically recognized by their file extensions .gz, .bz2 or .xz.

py-xxhash

2.0.2_gcc-9.4.0

xxhash is a Python binding for the xxHash library by Yann Collet.

py-yarl

1.7.2_gcc-9.4.0

The module provides handy URL class for URL parsing and changing.

py-youtube-dl

2021.12.17_gcc-9.4.0

Command-line program to download videos from YouTube.com and other video sites.

py-zipp

3.6.0_gcc-9.4.0

Backport of pathlib-compatible object wrapper for zip files.

py-zope-event

4.5.0_gcc-9.4.0

Very basic event publishing system.

py-zope-interface

5.4.0_gcc-9.4.0

This package provides an implementation of 'object interfaces' for Python. Interfaces are a mechanism for labeling objects as conforming to a given API or contract. So, this package can be considered as implementation of the Design By Contract methodology support in Python.

qhull

2020.2_gcc-9.4.0

Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, halfspace intersection about a point, furt hest-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. It handles roundoff errors from floating point arithmetic. It computes volumes, surface areas, and approximations to the convex hull.

qrupdate

1.1.2_gcc-9.4.0

qrupdate is a Fortran library for fast updates of QR and Cholesky decompositions.

qt

4.8.7_gcc-9.4.0
5.15.2_gcc-9.4.0

Qt is a comprehensive cross-platform C++ application framework.

quantum-espresso

7.0_gcc-9.4.0

Quantum ESPRESSO is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials.

qwt

6.1.6_gcc-9.4.0

The Qwt library contains GUI Components and utility classes which are primarily useful for programs with a technical background. Beside a framework for 2D plots it provides scales, sliders, dials, compasses, thermometers, wheels and knobs to control or display values, arrays, or ranges of type double.

r

4.1.3_gcc-9.4.0

R is 'GNU S', a freely available language and environment for statistical computing and graphics which provides a wide variety of statistical and graphical techniques: linear and nonlinear modelling, statistical tests, time series analysis, classification, clustering, etc. Please consult the R project homepage for further information.

r-abind

1.4-5_gcc-9.4.0

Combine Multidimensional Arrays.

r-ade4

1.7-18_gcc-9.4.0

Exploratory and Euclidean Methods in Environmental Sciences.

r-adegenet

2.1.5_gcc-9.4.0

Exploratory Analysis of Genetic and Genomic Data.

r-adegraphics

1.0-16_gcc-9.4.0

An S4 Lattice-Based Package for the Representation of Multivariate Data.

r-adephylo

1.1-11_gcc-9.4.0

Exploratory Analyses for the Phylogenetic Comparative Method.

r-adespatial

0.3-14_gcc-9.4.0

Multivariate Multiscale Spatial Analysis.

r-adgoftest

0.3_gcc-9.4.0

Anderson-Darling GoF test.

r-affy

1.72.0_gcc-9.4.0

Methods for Affymetrix Oligonucleotide Arrays.

r-affyio

1.64.0_gcc-9.4.0

Tools for parsing Affymetrix data files.

randrproto

1.5.0_gcc-9.4.0

X Resize and Rotate Extension (RandR).

r-annotate

1.72.0_gcc-9.4.0

Annotation for microarrays.

r-annotationdbi

1.56.2_gcc-9.4.0

Manipulation of SQLite-based annotations in Bioconductor.

r-annotationfilter

1.18.0_gcc-9.4.0

Facilities for Filtering Bioconductor Annotation Resources.

r-annotationhub

3.2.1_gcc-9.4.0

Client to access AnnotationHub resources.

r-aod

1.3.1_gcc-9.4.0

Analysis of Overdispersed Data.

r-ape

5.6-1_gcc-9.4.0

Analyses of Phylogenetics and Evolution.

rapidjson

1.2.0-2021-08-13_gcc-9.4.0

A fast JSON parser/generator for C++ with both SAX/DOM style API

r-aroma-light

3.24.0_gcc-9.4.0

Light-Weight Methods for Normalization and Visualization of Microarray Data using Only Basic R Data Types.

r-askpass

1.1_gcc-9.4.0

Safe Password Entry for R, Git, and SSH.

r-assertthat

0.2.1_gcc-9.4.0

Easy Pre and Post Assertions.

r-backports

1.4.1_gcc-9.4.0

Reimplementations of Functions Introduced Since R-3.0.0.

r-base64

2.0_gcc-9.4.0

Base64 Encoder and Decoder.

r-base64enc

0.1-3_gcc-9.4.0

Tools for base64 encoding.

r-bayesplot

1.8.1_gcc-9.4.0

Plotting for Bayesian Models.

r-beachmat

2.10.0_gcc-9.4.0

Compiling Bioconductor to Handle Each Matrix Type.

r-beanplot

1.2_gcc-9.4.0

Visualization via Beanplots (like Boxplot/Stripchart/Violin Plot).

r-beeswarm

0.4.0_gcc-9.4.0

The Bee Swarm Plot, an Alternative to Stripchart.

r-bh

1.78.0-0_gcc-9.4.0

Boost C++ Header Files.

r-biasedurn

1.07_gcc-9.4.0

Biased Urn Model Distributions.

r-biobase

2.54.0_gcc-9.4.0

Biobase: Base functions for Bioconductor.

r-biocfilecache

2.2.1_gcc-9.4.0

Manage Files Across Sessions.

r-biocgenerics

0.40.0_gcc-9.4.0

S4 generic functions used in Bioconductor.

r-biocio

1.4.0_gcc-9.4.0

Standard Input and Output for Bioconductor Packages.

r-biocmanager

1.30.16_gcc-9.4.0

Access the Bioconductor Project Package Repository.

r-biocneighbors

1.12.0_gcc-9.4.0

Nearest Neighbor Detection for Bioconductor Packages.

r-biocparallel

1.28.3_gcc-9.4.0

Bioconductor facilities for parallel evaluation.

r-biocsingular

1.10.0_gcc-9.4.0

Singular Value Decomposition for Bioconductor Packages.

r-biocversion

3.14.0_gcc-9.4.0

Set the appropriate version of Bioconductor packages.

r-biomart

2.50.3_gcc-9.4.0

Interface to BioMart databases (i.e. Ensembl).

r-biomartr

0.9.2_gcc-9.4.0

Genomic Data Retrieval.

r-biostrings

2.62.0_gcc-9.4.0

Efficient manipulation of biological strings.

r-biovizbase

1.42.0_gcc-9.4.0

Basic graphic utilities for visualization of genomic data.

r-bit

4.0.4_gcc-9.4.0

Classes and Methods for Fast Memory-Efficient Boolean Selections.

r-bit64

4.0.5_gcc-9.4.0

A S3 Class for Vectors of 64bit Integers.

r-bitops

1.0-7_gcc-9.4.0

Bitwise Operations.

r-blavaan

0.4-1_gcc-9.4.0

Bayesian Latent Variable Analysis.

r-blob

1.2.2_gcc-9.4.0

A Simple S3 Class for Representing Vectors of Binary Data ('BLOBS').

r-bluster

1.6.0_gcc-9.4.0

Clustering Algorithms for Bioconductor.

r-bmp

0.3_gcc-9.4.0

Read Windows Bitmap (BMP) Images.

r-boot

1.3-28_gcc-9.4.0

Bootstrap Functions (Originally by Angelo Canty for S).

r-brew

1.0-6_gcc-9.4.0

Templating Framework for Report Generation.

r-bridgesampling

1.1-2_gcc-9.4.0

Bridge Sampling for Marginal Likelihoods and Bayes Factors.

r-brio

1.1.3_gcc-9.4.0

Basic R Input Output.

r-brms

2.16.3_gcc-9.4.0

Bayesian Regression Models using 'Stan'.

r-brobdingnag

1.2-7_gcc-9.4.0

Very Large Numbers in R.

r-broom

0.7.12_gcc-9.4.0

Convert Statistical Objects into Tidy Tibbles.

r-bsgenome

1.62.0_gcc-9.4.0

Software infrastructure for efficient representation of full genomes and their SNPs.

r-bsgenome-hsapiens-ucsc-hg19

1.4.3_gcc-9.4.0

Full genome sequences for Homo sapiens (UCSC version hg19, based on GRCh37.p13).

r-bslib

0.3.1_gcc-9.4.0

Custom 'Bootstrap' 'Sass' Themes for 'shiny' and 'rmarkdown'.

r-bsseq

1.30.0_gcc-9.4.0

Analyze, manage and store bisulfite sequencing data.

r-bumphunter

1.36.0_gcc-9.4.0

Bump Hunter.

r-cachem

1.0.6_gcc-9.4.0

Cache R Objects with Automatic Pruning.

r-callr

3.7.0_gcc-9.4.0

Call R from R.

r-car

3.0-12_gcc-9.4.0

Companion to Applied Regression.

r-cardata

3.0-5_gcc-9.4.0

Companion to Applied Regression Data Sets.

r-caret

6.0-90_gcc-9.4.0

Classification and Regression Training.

r-catools

1.18.2_gcc-9.4.0

Moving Window Statistics, GIF, Base64, ROC AUC, etc.

r-cellranger

1.1.0_gcc-9.4.0

Translate Spreadsheet Cell Ranges to Rows and Columns.

r-champ

2.24.0_gcc-9.4.0

Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC.

r-champdata

2.26.0_gcc-9.4.0

Packages for ChAMP package.

r-checkmate

2.0.0_gcc-9.4.0

Fast and Versatile Argument Checks.

r-class

7.3-20_gcc-9.4.0

Functions for Classification.

r-classint

0.4-3_gcc-9.4.0

Choose Univariate Class Intervals.

r-cli

3.2.0_gcc-9.4.0

Helpers for Developing Command Line Interfaces.

r-clipr

0.7.1_gcc-9.4.0

Read and Write from the System Clipboard.

r-clue

0.3-60_gcc-9.4.0

Cluster Ensembles.

r-cluster

2.1.2_gcc-9.4.0

'Finding Groups in Data': Cluster Analysis Extended Rousseeuw et al.

r-cmdstanr

0.5.1_gcc-9.4.0

R Interface to 'CmdStan'.

r-coda

0.19-4_gcc-9.4.0

Output Analysis and Diagnostics for MCMC.

r-codetools

0.2-18_gcc-9.4.0

Code analysis tools for R.

r-codex

1.26.0_gcc-9.4.0

A Normalization and Copy Number Variation Detection Method for Whole Exome Sequencing.

r-colorspace

2.0-2_gcc-9.4.0

A Toolbox for Manipulating and Assessing Colors and Palettes.

r-colourpicker

1.1.1_gcc-9.4.0

A Colour Picker Tool for Shiny and for Selecting Colours in Plots.

r-combinat

0.0-8_gcc-9.4.0

combinatorics utilities.

r-commonmark

1.7_gcc-9.4.0

High Performance CommonMark and Github Markdown Rendering in R.

r-compquadform

1.4.3_gcc-9.4.0

Distribution Function of Quadratic Forms in Normal Variables.

r-copula

1.0-1_gcc-9.4.0

Multivariate Dependence with Copulas.

r-covr

3.5.1_gcc-9.4.0

Test Coverage for Packages.

r-cowplot

1.1.1_gcc-9.4.0

Streamlined Plot Theme and Plot Annotations for 'ggplot2'.

r-cpp11

0.4.2_gcc-9.4.0

A C++11 Interface for R's C Interface.

r-crayon

1.4.2_gcc-9.4.0

Colored Terminal Output.

r-credentials

1.3.2_gcc-9.4.0

Tools for Managing SSH and Git Credentials.

r-crosstalk

1.2.0_gcc-9.4.0

Inter-Widget Interactivity for HTML Widgets.

r-cubature

2.0.4.2_gcc-9.4.0

Adaptive multivariate integration over hypercubes.

r-curl

4.3.2_gcc-9.4.0

A Modern and Flexible Web Client for R.

r-data-table

1.14.2_gcc-9.4.0

Extension of `data.frame`.

r-dbi

1.1.2_gcc-9.4.0

R Database Interface.

r-dbplyr

2.1.1_gcc-9.4.0

A 'dplyr' Back End for Databases.

r-delayedarray

0.20.0_gcc-9.4.0

A unified framework for working transparently with on-disk and in-memory array-like datasets.

r-delayedmatrixstats

1.16.0_gcc-9.4.0

Functions that Apply to Rows and Columns of 'DelayedMatrix' Objects.

r-deldir

1.0-6_gcc-9.4.0

Delaunay Triangulation and Dirichlet (Voronoi) Tessellation.

r-dendextend

1.15.2_gcc-9.4.0

Extending 'Dendrogram' Functionality in R.

r-desc

1.4.0_gcc-9.4.0

Manipulate DESCRIPTION Files.

r-deseq2

1.34.0_gcc-9.4.0

Differential gene expression analysis based on the negative binomial distribution.

r-devtools

2.4.3_gcc-9.4.0

Tools to Make Developing R Packages Easier.

r-diagrammer

1.0.8_gcc-9.4.0

Graph/Network Visualization.

r-dichromat

2.0-0_gcc-9.4.0

Color Schemes for Dichromats.

r-diffobj

0.3.5_gcc-9.4.0

Diffs for R Objects.

r-digest

0.6.29_gcc-9.4.0

Create Compact Hash Digests of R Objects.

r-distributional

0.3.0_gcc-9.4.0

Functions for Base Types and Core R and 'Tidyverse' Features.

rdma-core

39.0_gcc-9.4.0

RDMA core userspace libraries and daemons

r-dmrcate

2.8.5_gcc-9.4.0

Methylation array and sequencing spatial analysis methods.

r-dnacopy

1.68.0_gcc-9.4.0

DNA copy number data analysis.

r-doparallel

1.0.16_gcc-9.4.0

Foreach Parallel Adaptor for the 'parallel' Package.

r-dorng

1.8.2_gcc-9.4.0

Generic Reproducible Parallel Backend for 'foreach' Loops.

r-downloader

0.4_gcc-9.4.0

Download Files over HTTP and HTTPS.

r-dplyr

1.0.7_gcc-9.4.0

A Grammar of Data Manipulation.

r-dqrng

0.3.0_gcc-9.4.0

Fast Pseudo Random Number Generators.

r-dss

2.42.0_gcc-9.4.0

Dispersion shrinkage for sequencing data.

r-dt

0.20_gcc-9.4.0

A Wrapper of the JavaScript Library 'DataTables'.

r-dtplyr

1.2.1_gcc-9.4.0

Data Table Back-End for 'dplyr'.

r-dygraphs

1.1.1.6_gcc-9.4.0

Interface to 'Dygraphs' Interactive Time Series Charting Library.

r-e1071

1.7-9_gcc-9.4.0

Misc Functions of the Department of Statistics, Probability Theory Group (Formerly: E1071), TU Wien.

re2

2021-06-01_gcc-9.4.0

RE2 is a fast, safe, thread-friendly alternative to backtracking regular expression engines like those used in PCRE, Perl, and Python.

readline

8.1_gcc-9.4.0

The GNU Readline library provides a set of functions for use by applications that allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. The Readline library includes additional functions to maintain a list of previously-entered command lines, to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.

recordproto

1.14.2_gcc-9.4.0

X Record Extension.

r-edger

3.36.0_gcc-9.4.0

Empirical Analysis of Digital Gene Expression Data in R.

reditools

1.3_2020-08-03_gcc-9.4.0

REDItools: python scripts for RNA editing detection by RNA-Seq data.

r-effects

4.2-1_gcc-9.4.0

Effect Displays for Linear, Generalized Linear, and Other Models.

relion

3.1.3_gcc-9.4.0
4.0-beta_gcc-9.4.0

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).

r-ellipsis

0.3.2_gcc-9.4.0

Tools for Working with ...

renderproto

0.11.1_gcc-9.4.0

X Rendering Extension.

r-ensembldb

2.18.3_gcc-9.4.0

Utilities to create and use Ensembl-based annotation databases.

repeatmasker

4.1.2-p1_gcc-9.4.0

RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.

r-estimability

1.3_gcc-9.4.0

Tools for Assessing Estimability of Linear Predictions.

r-evaluate

0.14_gcc-9.4.0

Parsing and Evaluation Tools that Provide More Details than the Default.

r-exomecopy

1.40.0_gcc-9.4.0

Copy number variant detection from exome sequencing read depth.

r-exomedepth

1.1.15_gcc-9.4.0

Calls Copy Number Variants from Targeted Sequence Data.

r-experimenthub

2.2.1_gcc-9.4.0

Client to access ExperimentHub resources.

r-fansi

1.0.2_gcc-9.4.0

ANSI Control Sequence Aware String Functions.

r-farver

2.1.0_gcc-9.4.0

High Performance Colour Space Manipulation.

r-fastcluster

1.2.3_gcc-9.4.0

Fast Hierarchical Clustering Routines for R and 'Python'.

r-fastica

1.2-3_gcc-9.4.0

FastICA Algorithms to Perform ICA and Projection Pursuit.

r-fastmap

1.1.0_gcc-9.4.0

Fast Implementation of a Key-Value Store.

r-fastmatch

1.1-3_gcc-9.4.0

Fast 'match()' Function.

r-fdb-infiniummethylation-hg18

2.2.0_gcc-9.4.0

Annotation package for Illumina Infinium DNA methylation probes.

r-fdb-infiniummethylation-hg19

2.2.0_gcc-9.4.0

Annotation package for Illumina Infinium DNA methylation probes.

r-filelock

1.0.2_gcc-9.4.0

Portable File Locking.

r-fitdistrplus

1.1-6_gcc-9.4.0

Help to Fit of a Parametric Distribution to Non-Censored or Censored Data.

r-fnn

1.1.3_gcc-9.4.0

Fast Nearest Neighbor Search Algorithms and Applications.

r-fontawesome

0.2.2_gcc-9.4.0

Easily Work with 'Font Awesome' Icons.

r-forcats

0.5.1_gcc-9.4.0

Tools for Working with Categorical Variables (Factors).

r-foreach

1.5.2_gcc-9.4.0

Provides Foreach Looping Construct.

r-foreign

0.8-82_gcc-9.4.0

Read Data Stored by 'Minitab', 'S', 'SAS', 'SPSS', 'Stata', 'Systat', 'Weka', 'dBase', ...

r-formatr

1.11_gcc-9.4.0

Format R Code Automatically.

r-formula

1.2-4_gcc-9.4.0

Extended Model Formulas.

r-fs

1.5.2_gcc-9.4.0

Cross-Platform File System Operations Based on 'libuv'.

r-futile-logger

1.4.3_gcc-9.4.0

A Logging Utility for R.

r-futile-options

1.0.1_gcc-9.4.0

Futile Options Management.

r-future

1.24.0_gcc-9.4.0

Unified Parallel and Distributed Processing in R for Everyone.

r-future-apply

1.8.1_gcc-9.4.0

Apply Function to Elements in Parallel using Futures.

r-gargle

1.2.0_gcc-9.4.0

Utilities for Working with Google APIs.

r-gdata

2.18.0_gcc-9.4.0

Various R Programming Tools for Data Manipulation.

r-genefilter

1.76.0_gcc-9.4.0

Methods for filtering genes from high-throughput experiments.

r-genelendatabase

1.30.0_gcc-9.4.0

Lengths of mRNA transcripts for a number of genomes.

r-geneplotter

1.72.0_gcc-9.4.0

Graphics related functions for Bioconductor.

r-generics

0.1.1_gcc-9.4.0

Common S3 Generics not Provided by Base R Methods Related to Model Fitting.

r-genomeinfodb

1.30.1_gcc-9.4.0

Utilities for manipulating chromosome names, including modifying them to follow a particular naming style.

r-genomeinfodbdata

1.2.7_gcc-9.4.0

for mapping between NCBI taxonomy ID and species. Used by functions in the GenomeInfoDb package.

r-genomicalignments

1.30.0_gcc-9.4.0

Representation and manipulation of short genomic alignments.

r-genomicfeatures

1.46.4_gcc-9.4.0

Conveniently import and query gene models.

r-genomicranges

1.46.1_gcc-9.4.0

Representation and manipulation of genomic intervals.

r-geoquery

2.62.2_gcc-9.4.0

Get data from NCBI Gene Expression Omnibus (GEO).

r-gert

1.5.0_gcc-9.4.0

Simple Git Client for R.

r-getopt

1.20.3_gcc-9.4.0

C-Like 'getopt' Behavior.

r-ggbeeswarm

0.6.0_gcc-9.4.0

Categorical Scatter (Violin Point) Plots.

r-ggmap

3.0.0_gcc-9.4.0

Spatial Visualization with ggplot2.

r-ggplot2

3.3.5_gcc-9.4.0

Create Elegant Data Visualisations Using the Grammar of Graphics.

r-ggrepel

0.9.1_gcc-9.4.0

Repulsive Text and Label Geoms for 'ggplot2'.

r-ggridges

0.5.3_gcc-9.4.0

Ridgeline Plots in 'ggplot2'.

r-ggvis

0.4.7_gcc-9.4.0

Interactive Grammar of Graphics.

r-gh

1.3.0_gcc-9.4.0

'GitHub' 'API'.

r-gitcreds

0.1.1_gcc-9.4.0

Query 'git' Credentials from 'R'.

r-glmgampoi

1.8.0_gcc-9.4.0

Fit a Gamma-Poisson Generalized Linear Model.

r-glmnet

4.1-3_gcc-9.4.0

Lasso and Elastic-Net Regularized Generalized Linear Models.

r-globals

0.14.0_gcc-9.4.0

Identify Global Objects in R Expressions.

r-globaltest

5.48.0_gcc-9.4.0

Testing Groups of Covariates/Features for Association with a Response Variable, with Applications to Gene Set Testing.

r-glue

1.6.1_gcc-9.4.0

Interpreted String Literals.

r-gmp

0.6-2.1_gcc-9.4.0

Multiple Precision Arithmetic.

r-go-db

3.14.0_gcc-9.4.0

A set of annotation maps describing the entire Gene Ontology.

r-goftest

1.2-3_gcc-9.4.0

Classical Goodness-of-Fit Tests for Univariate Distributions.

r-googledrive

2.0.0_gcc-9.4.0

An Interface to Google Drive.

r-googlesheets4

1.0.0_gcc-9.4.0

Access Google Sheets using the Sheets API V4.

r-googlevis

0.6.11_gcc-9.4.0

R Interface to Google Charts.

r-goseq

1.46.0_gcc-9.4.0

Gene Ontology analyser for RNA-seq and other length biased data.

r-gower

0.2.2_gcc-9.4.0

Gower's Distance.

r-gplots

3.1.1_gcc-9.4.0

Various R Programming Tools for Plotting Data.

r-gridextra

2.3_gcc-9.4.0

Miscellaneous Functions for 'Grid' Graphics.

r-gsalib

2.1_gcc-9.4.0

Utility Functions For GATK.

r-gsl

2.1-7.1_gcc-9.4.0

Wrapper for the Gnu Scientific Library.

r-gtable

0.3.0_gcc-9.4.0

Arrange 'Grobs' in Tables.

r-gtools

3.9.2_gcc-9.4.0

Various R Programming Tools.

r-gviz

1.38.3_gcc-9.4.0

Plotting data and annotation information along genomic coordinates.

r-hardhat

0.2.0_gcc-9.4.0

Construct Modeling Packages.

rhash

1.4.2_gcc-9.4.0

RHash is a console utility for computing and verifying hash sums of files. It supports CRC32, MD4, MD5, SHA1, SHA256, SHA512, SHA3, Tiger, TTH, Torrent BTIH, AICH, ED2K, GOST R 34.11-94, RIPEMD-160, HAS-160, EDON-R 256/512, WHIRLPOOL and SNEFRU hash sums.

r-haven

2.4.3_gcc-9.4.0

Import and Export 'SPSS', 'Stata' and 'SAS' Files.

r-hdf5array

1.22.1_gcc-9.4.0

HDF5 backend for DelayedArray objects.

r-hdf5r

1.3.5_gcc-9.4.0

Interface to the 'HDF5' Binary Data Format.

r-here

1.0.1_gcc-9.4.0

A Simpler Way to Find Your Files.

r-hh

3.1-47_gcc-9.4.0

Statistical Analysis and Data Display: Heiberger and Holland.

r-highr

0.9_gcc-9.4.0

Syntax Highlighting for R Source Code.

r-hmisc

4.6-0_gcc-9.4.0

Harrell Miscellaneous.

r-hms

1.1.1_gcc-9.4.0

Pretty Time of Day.

r-htmltable

2.4.0_gcc-9.4.0

Advanced Tables for Markdown/HTML.

r-htmltools

0.5.2_gcc-9.4.0

Tools for HTML.

r-htmlwidgets

1.5.4_gcc-9.4.0

HTML Widgets for R.

r-httpuv

1.6.5_gcc-9.4.0

HTTP and WebSocket Server Library.

r-httr

1.4.2_gcc-9.4.0

Tools for Working with URLs and HTTP.

r-ica

1.0-2_gcc-9.4.0

Independent Component Analysis.

r-ids

1.0.1_gcc-9.4.0

Generate Random Identifiers.

r-igraph

1.2.11_gcc-9.4.0

Network Analysis and Visualization.

r-illumina450probevariants-db

1.30.0_gcc-9.4.0

Annotation Package combining variant data from 1000 Genomes Project for Illumina HumanMethylation450 Bead Chip probes.

r-illuminahumanmethylation450kanno-ilmn12-hg19

0.6.0_gcc-9.4.0

Annotation for Illumina's 450k methylation arrays.

r-illuminahumanmethylation450kmanifest

0.4.0_gcc-9.4.0

Annotation for Illumina's 450k methylation arrays.

r-illuminahumanmethylationepicanno-ilm10b4-hg19

0.6.0_gcc-9.4.0

Annotation for Illumina's EPIC methylation arrays.

r-illuminahumanmethylationepicmanifest

0.3.0_gcc-9.4.0

Manifest for Illumina's EPIC methylation arrays.

r-illuminaio

0.36.0_gcc-9.4.0

Parsing Illumina Microarray Output Files.

r-imager

0.42.11_gcc-9.4.0

Image Processing Library Based on 'CImg'.

r-impute

1.68.0_gcc-9.4.0

impute: Imputation for microarray data.

r-influencer

0.1.0.1_gcc-9.4.0

Software Tools to Quantify Structural Importance of Nodes in a Network.

r-ini

0.3.1_gcc-9.4.0

Read and Write '.ini' Files.

r-inline

0.3.19_gcc-9.4.0

Functions to Inline C, C++, Fortran Function Calls from R.

r-insight

0.16.0_gcc-9.4.0

Easy Access to Model Information for Various Model Objects.

r-interactivedisplaybase

1.32.0_gcc-9.4.0

Base package for enabling powerful shiny web displays of Bioconductor objects.

r-ipred

0.9-12_gcc-9.4.0

Improved Predictors.

r-iranges

2.28.0_gcc-9.4.0

Foundation of integer range manipulation in Bioconductor.

r-irlba

2.3.5_gcc-9.4.0

Fast Truncated Singular Value Decomposition and Principal Components Analysis for Large Dense and Sparse Matrices.

r-isoband

0.2.5_gcc-9.4.0

Generate Isolines and Isobands from Regularly Spaced Elevation Grids.

r-isva

1.9_gcc-9.4.0

Independent Surrogate Variable Analysis.

r-iterators

1.0.13_gcc-9.4.0

Provides Iterator Construct.

r-jade

2.0-3_gcc-9.4.0

Blind Source Separation Methods Based on Joint Diagonalization and Some BSS Performance Criteria.

r-jpeg

0.1-9_gcc-9.4.0

Read and write JPEG images.

r-jquerylib

0.1.4_gcc-9.4.0

Obtain 'jQuery' as an HTML Dependency Object.