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'contrib/doc' section

/contrib/bcbio/bcbio-doc

Documentation for RNAseq-workflows of bcbio(-nextgen)

This package provides the documentation for all aspects of the workflows and technology of the bcbio-nextgen toolkit. . A high-level configuration file specifies inputs and analysis parameters to drive a parallel pipeline that handles distributed execution, idempotent processing restarts and safe transactional steps. The project contributes a shared community resource that handles the data processing component of sequencing analysis, providing researchers with more time to focus on the downstream biology.


Bayesian MCMC phylogenetic inference - example data

BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. Included is a simple to use user-interface program for setting up standard analyses and a suit of programs for analysing the results. . This package contains the example data.


Bayesian MCMC phylogenetic inference - documentation

BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. Included is a simple to use user-interface program for setting up standard analyses and a suit of programs for analysing the results. . This package contains the documentation.

/contrib/cltl/cltl

Common Lisp the Language, second edition, book (Pre-ANSI)

This package installs the HTML version of Guy L. Steele book Common Lisp the Language, second edition. This book describes a snapshot of the Common Lisp language during the period that the ANSI Common Lisp standard was created. Thus, this book describe a NON-STANDARD version of Common Lisp which is similar to, but is *NOT*, ANSI Common Lisp. . For reference on ANSI Common Lisp, use the Debian package "hyperspec". This book is included in Debian because, while it does differ from the ANSI standard, it has more details than the "hyperspec" about the design and usage of Lisp. . This package does not contain the actual HTML files, but rather downloads the HTML archive from the Internet and then installs it.


documentation for the GNU compilers (gcc, gobjc, g++)

This is the dependency package that should install manual pages and documentation for Debian default version of GNU compilers. . This documentation is available from non-free part of Debian archive.


documentation for the GNU Go compiler (gccgo)

This is the dependency package that should install documentation for Debian default version of GNU Go compiler. . This documentation is available from non-free part of Debian archive.


documentation for the GNU Ada Compiler (gnat)

This is the dependency package that should install documentation for Debian default version of GNU Ada compiler. . This documentation is available from non-free part of Debian archive.


several GNU manual pages

This package provides gfdl.7, gpl.7, and fsf-funding.7 manual pages, which should be available together with gcc man pages to fit GNU Free Documentation License requirements.


documentation for the GNU Fortran Compiler (gfortran)

This is the dependency package that should install manual page and documentation for Debian default version of GNU Fortran compiler. . This documentation is available from non-free part of Debian archive.


documentation for the GNU Java tools (gcj, gij)

This is the dependency package that should install documentation for Debian default version of GNU Java tools. . This documentation is available from non-free part of Debian archive.


documentation for the GNU C preprocessor (cpp)

This is the dependency package that should install manual page and documentation for Debian default version of GNU C preprocessor. . This documentation is available from non-free part of Debian archive.

/contrib/gemrb/gemrb-doc

Documentation for GemRB

GemRB (Game Engine Made with preRendered Background) is a new implementation of the original Infinity Engine (the one of Baldur's Gate, Icewind Dale, Planescape: Torment, ...) to Linux/Unix, MacOS X and Windows with some enhancements. . This package contains documentation about GemRB and how to write custom games.

/contrib/hyperspec/hyperspec

Common Lisp ANSI-standard Hyperspec

This is a installer package for the html-ed version of the ANSI standard for Common Lisp. Note that these pages are only FYI and are not valid as a reference. But for all intents and purposes this is a good enough reference for daily work.

/contrib/ifeffit/ifeffit-doc

IFEFFIT examples and documentation

This package contains all the available documentation for IFEFFIT and its component programs. Example files for EXAFS data analysis are also provided as tutorials.

/contrib/magma/libmagma-doc

Matrix Algebra on GPU and Multicore Architectures (doc)

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. . The MAGMA research is based on the idea that, to address the complex challenges of the emerging hybrid environments, optimal software solutions will themselves have to hybridize, combining the strengths of different algorithms within a single framework. Building on this idea, we aim to design linear algebra algorithms and frameworks for hybrid manycore and GPU systems that can enable applications to fully exploit the power that each of the hybrid components offers. . This package contains the Doxygen HTML documentation.

/contrib/mtj/libmtj-java-doc

Java library for developing numerical applications (documentation)

MTJ is designed to be used as a library for developing numerical applications, both for small and large scale computations. The library is based on BLAS and LAPACK for its dense and structured sparse computations, and on the Templates project for unstructured sparse operations. . MTJ uses the netlib-java project as a backend, which can be set up to use machine-optimised BLAS libraries for improved performance of dense matrix operations, falling back to a pure Java implementation. This ensures perfect portability, while allowing for improved performance in a production environment. . This package contains the javadoc documentation files.


module to access Nvidia‘s CUDA computation API (documentation)

PyCUDA lets you access Nvidia‘s CUDA parallel computation API from Python. Several wrappers of the CUDA API already exist–so what’s so special about PyCUDA? * Object cleanup tied to lifetime of objects. This idiom, often called RAII in C++, makes it much easier to write correct, leak- and crash-free code. PyCUDA knows about dependencies, too, so (for example) it won’t detach from a context before all memory allocated in it is also freed. * Convenience. Abstractions like pycuda.driver.SourceModule and pycuda.gpuarray.GPUArray make CUDA programming even more convenient than with Nvidia’s C-based runtime. * Completeness. PyCUDA puts the full power of CUDA’s driver API at your disposal, if you wish. * Automatic Error Checking. All CUDA errors are automatically translated into Python exceptions. * Speed. PyCUDA’s base layer is written in C++, so all the niceties above are virtually free. * Helpful Documentation. . This package contains HTML documentation and example scripts.


Documentation for the Python LDAP interface module

This module provides a Python interface to the OpenLDAP client library (LDAP is the Lightweight Directory Access Protocol). . This package contains the HTML documentation for the module.


analysis of small RNA in NGS data (documentation)

Seqcluster investigates small RNA sequences of all sorts in RNA sequencing data. This is especially helpful for the identification of RNA that is neither coding nor belonging to the already well-established group of miRNA, towards many tools feel constrained to. . This package provides the HTML documentation for the Python-implemented seqcluster tool.

/contrib/sus/susv2

Fetch and install SUSv2

The Single Unix Specifications are not permitted to be generally redistributed, so this is an installer that fetches them and installs them in a Debian appropriate way. This installer will fetch and install Single Unix Specification v2.

/contrib/sus/susv3

Fetch and install SUSv3

The Single Unix Specifications are not permitted to be generally redistributed, so this is an installer that fetches them and installs them in a Debian appropriate way. This installer will fetch and install POSIX:2001 (also known as Single Unix Specification v3) with the POSIX:2004 Technical Corrigendum 1 and 2.

/contrib/sus/susv4

Fetch and install SUSv4 (POSIX.1-2017)

The Single Unix Specifications are not permitted to be generally redistributed, so this is an installer that fetches them and installs them in a Debian appropriate way. This installer will fetch and install POSIX.1-2017 (variously also known as IEEE Std 1003.1-2017, The Open Group Base Specifications Issue 7, 2018 Edition, or Single Unix Specification v4, 2018 edition).

/contrib/zfs-linux/pyzfs-doc

wrapper for libzfs_core C library (documentation)

libzfs_core is intended to be a stable interface for programmatic administration of ZFS. This wrapper provides one-to-one wrappers for libzfs_core API functions, but the signatures and types are more natural to Python. . nvlists are wrapped as dictionaries or lists depending on their usage. Some parameters have default values depending on typical use for increased convenience. Enumerations and bit flags become strings and lists of strings in Python. Errors are reported as exceptions rather than integer errno-style error codes. The wrapper takes care to provide one-to-many mapping of the error codes to the exceptions by interpreting a context in which the error code is produced. . This package contains the documentation.