tools
Archive-Zip
https://metacpan.org/pod/Archive::Zip
Package description
Provide an interface to ZIP archive files.
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AutoDock
Package description
AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.
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AutoDock-GPU
https://github.com/ccsb-scripps/AutoDock-GPU
Package description
OpenCL and Cuda accelerated version of AutoDock. It leverages its embarrasingly parallelizable LGA by processing ligand-receptor poses in parallel over multiple compute units. AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.
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DAlpahBall
https://www.rosettacommons.org/
Package description
AlphaBall contains a suite of program for computing the surface area and volume of unions of balls. It works on millions of balls. Part of Rosetta in main/source/extras
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DB
https://www.oracle.com/technetwork/products/berkeleydb
Package description
Berkeley DB enables the development of custom data management solutions, without the overhead traditionally associated with such custom projects.
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EasyBuild
https://easybuilders.github.io/easybuild
Package description
EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.
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GLPK
https://www.gnu.org/software/glpk/
Package description
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.
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Ghostscript
Package description
Ghostscript is a versatile processor for PostScript data with the ability to render PostScript to different targets. It used to be part of the cups printing stack, but is no longer used for that.
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HPL
https://www.netlib.org/benchmark/hpl/
Package description
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.
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IOR
Package description
The IOR software is used for benchmarking parallel file systems using POSIX, MPIIO, or HDF5 interfaces.
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IPython
https://ipython.org/index.html
Package description
IPython provides a rich architecture for interactive computing with: Powerful interactive shells (terminal and Qt-based). A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. Support for interactive data visualization and use of GUI toolkits. Flexible, embeddable interpreters to load into your own projects. Easy to use, high performance tools for parallel computing.
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IRkernel
Package description
The R kernel for the 'Jupyter' environment executes R code which the front-end (Jupyter Notebook or other front-ends) submits to the kernel via the network.
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JupyterLab
Package description
JupyterLab is the next-generation user interface for Project Jupyter offering all the familiar building blocks of the classic Jupyter Notebook (notebook, terminal, text editor, file browser, rich outputs, etc.) in a flexible and powerful user interface. JupyterLab will eventually replace the classic Jupyter Notebook.
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Meson
Package description
Meson is a cross-platform build system designed to be both as fast and as user friendly as possible.
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Nextflow
Package description
Nextflow is a reactive workflow framework and a programming DSL that eases writing computational pipelines with complex data
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Ninja
Package description
Ninja is a small build system with a focus on speed.
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Pandoc
Package description
If you need to convert files from one markup format into another, pandoc is your swiss-army knife
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Pint
https://pypi.python.org/pypi/pint
Package description
Physical quantities module
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Szip
https://www.hdfgroup.org/doc_resource/SZIP/
Package description
Szip compression software, providing lossless compression of scientific data
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UnZip
http://www.info-zip.org/UnZip.html
Package description
UnZip is an extraction utility for archives compressed in .zip format (also called "zipfiles"). Although highly compatible both with PKWARE's PKZIP and PKUNZIP utilities for MS-DOS and with Info-ZIP's own Zip program, our primary objectives have been portability and non-MSDOS functionality.
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Vim
Package description
Vim is an advanced text editor that seeks to provide the power of the de-facto Unix editor 'Vi', with a more complete feature set.
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Wireshark
Package description
Wireshark is the world's foremost and widely-used network protocol analyzer. It lets you see what's happening on your network at a microscopic level and is the de facto (and often de jure) standard across many commercial and non-profit enterprises, government agencies, and educational institutions.
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XZ
Package description
xz: XZ utilities
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Z3
https://github.com/Z3Prover/z3
Package description
Z3 is a theorem prover from Microsoft Research.
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Zip
http://www.info-zip.org/Zip.html
Package description
Zip is a compression and file packaging/archive utility. Although highly compatible both with PKWARE's PKZIP and PKUNZIP utilities for MS-DOS and with Info-ZIP's own UnZip, our primary objectives have been portability and other-than-MSDOS functionality
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archspec
https://github.com/archspec/archspec
Package description
A library for detecting, labeling, and reasoning about microarchitectures
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arrow-R
https://cran.r-project.org/web/packages/arrow
Package description
R interface to the Apache Arrow C++ library
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awscli
https://pypi.python.org/pypi/awscli
Package description
Universal Command Line Environment for AWS
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binutils
https://directory.fsf.org/project/binutils/
Package description
binutils: GNU binary utilities
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bokeh
https://github.com/bokeh/bokeh
Package description
Statistical and novel interactive HTML plots for Python
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bzip2
Package description
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.
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cURL
Package description
libcurl is a free and easy-to-use client-side URL transfer library, supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, Kerberos), file transfer resume, http proxy tunneling and more.
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ccache
Package description
Ccache (or “ccache”) is a compiler cache. It speeds up recompilation by caching previous compilations and detecting when the same compilation is being done again
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cppy
https://github.com/nucleic/cppy
Package description
A small C++ header library which makes it easier to write Python extension modules. The primary feature is a PyObject smart pointer which automatically handles reference counting and provides convenience methods for performing common object operations.
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deepdiff
https://deepdiff.readthedocs.io/en/latest/
Package description
DeepDiff: Deep Difference of dictionaries, iterables and almost any other object recursively.
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enchant-2
https://github.com/AbiWord/enchant
Package description
Enchant aims to provide a simple but comprehensive abstraction for dealing with different spell checking libraries in a consistent way. A client, such as a text editor or word processor, need not know anything about a specific spell-checker, and since all back-ends are plugins, new spell-checkers can be added without needing any change to the program using Enchant.
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expat
Package description
Expat is an XML parser library written in C. It is a stream-oriented parser in which an application registers handlers for things the parser might find in the XML document (like start tags).
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expecttest
https://github.com/ezyang/expecttest
Package description
This library implements expect tests (also known as "golden" tests). Expect tests are a method of writing tests where instead of hard-coding the expected output of a test, you run the test to get the output, and the test framework automatically populates the expected output. If the output of the test changes, you can rerun the test with the environment variable EXPECTTEST_ACCEPT=1 to automatically update the expected output.
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fio
Package description
Flexible I/O tester
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gawk
https://www.gnu.org/software/gawk
Package description
The awk utility interprets a special-purpose programming language that makes it possible to handle simple data-reformatting jobs with just a few lines of code.
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gettext
https://www.gnu.org/software/gettext/
Package description
GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation
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git
Package description
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.
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git-lfs
Package description
Git Large File Storage (LFS) replaces large files such as audio samples, videos, datasets, and graphics with text pointers inside Git, while storing the file contents on a remote server like GitHub.com
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googletest
https://github.com/google/googletest
Package description
Google's framework for writing C++ tests on a variety of platforms
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gperftools
https://github.com/gperftools/gperftools
Package description
gperftools is a collection of a high-performance multi-threaded malloc() implementation, plus some pretty nifty performance analysis tools. Includes TCMalloc, heap-checker, heap-profiler and cpu-profiler.
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groff
https://www.gnu.org/software/groff
Package description
Groff (GNU troff) is a typesetting system that reads plain text mixed with formatting commands and produces formatted output.
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gzip
https://www.gnu.org/software/gzip/
Package description
gzip (GNU zip) is a popular data compression program as a replacement for compress
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help2man
https://www.gnu.org/software/help2man/
Package description
help2man produces simple manual pages from the '--help' and '--version' output of other commands.
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hiredis
https://github.com/redis/hiredis
Package description
Hiredis is a minimalistic C client library for the Redis database. It is minimalistic because it just adds minimal support for the protocol, but at the same time it uses a high level printf-alike API in order to make it much higher level than otherwise suggested by its minimal code base and the lack of explicit bindings for every Redis command.
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hunspell
Package description
Hunspell is a spell checker and morphological analyzer library and program designed for languageswith rich morphology and complex word compounding or character encoding.
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hypothesis
https://github.com/HypothesisWorks/hypothesis
Package description
Hypothesis is an advanced testing library for Python. It lets you write tests which are parametrized by a source of examples, and then generates simple and comprehensible examples that make your tests fail. This lets you find more bugs in your code with less work.
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imbalanced-learn
https://github.com/scikit-learn-contrib/imbalanced-learn
Package description
imbalanced-learn is a Python package offering a number of re-sampling techniques commonly used in datasets showing strong between-class imbalance.
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jax
https://pypi.python.org/pypi/jax
Package description
Composable transformations of Python+NumPy programs: differentiate, vectorize, JIT to GPU/TPU, and more
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libarchive
Package description
Multi-format archive and compression library
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libavif
https://github.com/AOMediaCodec/libavif
Package description
This library aims to be a friendly, portable C implementation of the AV1 Image File Format, as described here: https://aomediacodec.github.io/av1-avif/
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networkx
https://pypi.python.org/pypi/networkx
Package description
NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks.
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nf-test
https://code.askimed.com/nf-test/
Package description
nf-test is a simple testing framework for Nextflow pipelines
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numactl
https://github.com/numactl/numactl
Package description
The numactl program allows you to run your application program on specific cpu's and memory nodes. It does this by supplying a NUMA memory policy to the operating system before running your program. The libnuma library provides convenient ways for you to add NUMA memory policies into your own program.
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parallel
https://savannah.gnu.org/projects/parallel/
Package description
parallel: Build and execute shell commands in parallel
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pigz
Package description
pigz, which stands for parallel implementation of gzip, is a fully functional replacement for gzip that exploits multiple processors and multiple cores to the hilt when compressing data. pigz was written by Mark Adler, and uses the zlib and pthread libraries.
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py-cpuinfo
https://github.com/workhorsy/py-cpuinfo
Package description
py-cpuinfo gets CPU info with pure Python.
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pydantic
https://pypi.python.org/pypi/pydantic
Package description
Data validation and settings management using python 3.6 type hinting
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pytest
Package description
pytest: simple powerful testing with Python
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pytest-xdist
https://github.com/pytest-dev/pytest-xdist
Package description
xdist: pytest distributed testing plugin The pytest-xdist plugin extends pytest with some unique test execution modes: * test run parallelization: if you have multiple CPUs or hosts you can use those for a combined test run. This allows to speed up development or to use special resources of remote machines. * --looponfail: run your tests repeatedly in a subprocess. After each run pytest waits until a file in your project changes and then re-runs the previously failing tests. This is repeated until all tests pass after which again a full run is performed. * Multi-Platform coverage: you can specify different Python interpreters or different platforms and run tests in parallel on all of them. Before running tests remotely, pytest efficiently “rsyncs” your program source code to the remote place. All test results are reported back and displayed to your local terminal. You may specify different Python versions and interpreters.
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quarto
Package description
An open-source scientific and technical publishing system
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re2c
Package description
re2c is a free and open-source lexer generator for C and C++. Its main goal is generating fast lexers: at least as fast as their reasonably optimized hand-coded counterparts. Instead of using traditional table-driven approach, re2c encodes the generated finite state automata directly in the form of conditional jumps and comparisons.
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snakemake
https://snakemake.readthedocs.io
Package description
The Snakemake workflow management system is a tool to create reproducible and scalable data analyses.
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tcsh
Package description
Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). It is a command language interpreter usable both as an interactive login shell and a shell script command processor. It includes a command-line editor, programmable word completion, spelling correction, a history mechanism, job control and a C-like syntax.
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unifdef
https://github.com/fanf2/unifdef
Package description
unifdef - selectively remove C preprocessor conditionals The unifdef utility selectively processes conditional C preprocessor and the additional text that they delimit, while otherwise leaving the file alone.
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util-linux
https://www.kernel.org/pub/linux/utils/util-linux
Package description
Set of Linux utilities
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wandb
Package description
CLI and Python API for Weights and Biases: a tool for visualizing and tracking your machine learning experiments.
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xxd
Package description
xxd is part of the VIM package and this will only install xxd, not vim! xxd converts to/from hexdumps of binary files.