Bug#901973: ITP: node-destroy -- Node.js stream destruction utility, with quirk handling
Control: owner -1 Shayan Doust -- Shayan Doust - 201427418 Fingerprint: 0401 A810 A6F2 4303 1EA3 9759 6D7D 4419 19D0 2395 Note: all emails sent by me are signed with my PGP key. signature.asc Description: PGP signature
Bug#901973: ITP: node-destroy -- Node.js stream destruction utility, with quirk handling
Hello, I will be packaging send-transform soon and this is a dependency. Any progress with this? If not, I'll package node-destroy. Kind regards, Shayan Doust On Wed, 20 Jun 2018 16:33:13 -0400 Zebulon McCorkle wrote: > Package: wnpp > Severity: wishlist > Owner: Zebulon McCorkle > > * Package name: node-destroy > Version : 1.0.4 > Upstream Author : Jonathan Ong > * URL : https://github.com/stream-utils/destroy > * License : MIT > Programming Lang: Node.js > Description : Node.js stream destruction utility, with quirk handling > > Maintained in pkg-javascript-devel > > -- Shayan Doust - 201427418 Fingerprint: 0401 A810 A6F2 4303 1EA3 9759 6D7D 4419 19D0 2395 Note: all emails sent by me are signed with my PGP key. signature.asc Description: PGP signature
Bug#990011: ITP: r-cran-xmlr -- Read, Write and Work with 'XML' Data
Package: wnpp Severity: wishlist X-Debbugs-Cc: he...@shayandoust.me Subject: ITP: r-cran-xmlr -- Read, Write and Work with 'XML' Data Package: wnpp Owner: Shayan Doust Severity: wishlist * Package name: r-cran-xmlr Version : 0.1.2 Upstream Author : Per Nyfelt, * URL : https://cran.r-project.org/package=xmlr * License : MIT Programming Lang: GNU R Description : Read, Write and Work with 'XML' Data 'XML' package for creating and reading and manipulating 'XML', with an object model based on 'Reference Classes'. Remark: This package is maintained by Debian R Packages Maintainers at https://salsa.debian.org/r-pkg-team/r-cran-xmlr
Bug#989850: ITP: python-flask-talisman -- HTTP security headers for Flask
Package: wnpp Severity: wishlist X-Debbugs-Cc: he...@shayandoust.me Subject: ITP: python-flask-talisman -- HTTP security headers for Flask Package: wnpp Owner: Shayan Doust Severity: wishlist * Package name: python-flask-talisman Version : 0.7.0 Upstream Author : Google Inc. * URL : https://github.com/GoogleCloudPlatform/flask-talisman * License : Apache-2.0 Programming Lang: Python Description : HTTP security headers for Flask Talisman is a small Flask extension that handles setting HTTP headers that can help protect against a few common web application security measures. Remark: This package is maintained by Debian Med Packaging Team at https://salsa.debian.org/med-team/flask-talisman
Bug#986386: ITP: r-cran-performanceanalytics -- GNU R Econometric Tools for Performance and Risk Analysis
Package: wnpp Severity: wishlist X-Debbugs-Cc: he...@shayandoust.me Subject: ITP: r-cran-performanceanalytics -- GNU R Econometric Tools for Performance and Risk Analysis Package: wnpp Owner: Shayan Doust Severity: wishlist * Package name: r-cran-performanceanalytics Version : 2.0.4 Upstream Author : Brian G. Peterson, * URL : https://cran.r-project.org/package=PerformanceAnalytics * License : GPL-2 Programming Lang: GNU R Description : GNU R Econometric Tools for Performance and Risk Analysis Collection of econometric functions for performance and risk analysis. In addition to standard risk and performance metrics, this package aims to aid practitioners and researchers in utilizing the latest research in analysis of non-normal return streams. In general, it is most tested on return (rather than price) data on a regular scale, but most functions will work with irregular return data as well, and increasing numbers of functions will work with P or price data where possible. Remark: This package is maintained by Debian R Packages Maintainers at https://salsa.debian.org/r-pkg-team/r-cran-performanceanalytics
Bug#977391: ITP: r-cran-bma -- Bayesian Model Averaging
Package: wnpp Severity: wishlist Subject: ITP: r-cran-bma -- Bayesian Model Averaging Package: wnpp Owner: Shayan Doust Severity: wishlist * Package name: r-cran-bma Version : 3.18.14 Upstream Author : Adrian Raftery , * URL : https://cran.r-project.org/package=BMA * License : GPL-2+ Programming Lang: GNU R Description : Bayesian Model Averaging Package for Bayesian model averaging and variable selection for linear models, generalized linear models and survival models (cox regression). Remark: This package is maintained by Debian R Packages Maintainers at https://salsa.debian.org/r-pkg-team/r-cran-bma
Bug#960906: shiny-server -- put Shiny web apps online
Hello Andreas, As of now, there still stands a single dependency called [node-http-proxy]. Unfortunately, it looks like it relies on socket.io, which has not been packaged yet. Kind regards, Shayan Doust [node-http-proxy]: https://salsa.debian.org/js-team/node-http-proxy/ OpenPGP_0x6D7D441919D02395.asc Description: application/pgp-keys OpenPGP_signature Description: OpenPGP digital signature
Bug#972392: ITP: r-cran-bios2cor -- GNU R from Biological Sequences and Simulations to Correlation
Package: wnpp Severity: wishlist Subject: ITP: r-cran-bios2cor -- GNU R from Biological Sequences and Simulations to Correlation Package: wnpp Owner: Shayan Doust Severity: wishlist * Package name: r-cran-bios2cor Version : 2.2 Upstream Author : Bruck Taddese, * URL : https://cran.r-project.org/package=Bios2cor * License : GPL-2+ Programming Lang: GNU R Description : GNU R from Biological Sequences and Simulations to Correlation Analysis Utilities for computation and analysis of correlation/covariation in multiple sequence alignments and in side chain motions during molecular dynamics simulations. Features include the computation of correlation/covariation scores using a variety of scoring functions between either sequence positions in alignments or side chain dihedral angles in molecular dynamics simulations and utilities to analyze the correlation/covariation matrix through a variety of tools including network representation and principal components analysis. In addition, several utility functions are based on the R graphical environment to provide friendly tools for help in data interpretation. Examples of sequence covariation analysis are provided in: (1) Pele J, Moreau M, Abdi H, Rodien P, Castel H, Chabbert M (2014) and (2) Taddese B, Deniaud M, Garnier A, Tiss A, Guissouma H, Abdi H, Henrion D, Chabbert M (2018) . An example of side chain correlated motion analysis is provided in: Taddese B, Garnier A, Abdi H, Henrion D, Chabbert M (2020) . This work was supported by the French National Research Agency (Grant number: ANR-11-BSV2-026) and by GENCI (Grant number: 100567). Remark: This package is maintained by Debian R Packages Maintainers at https://salsa.debian.org/r-pkg-team/r-cran-bios2cor
Bug#971699: ITP: r-cran-circular -- GNU R Circular Statistics
Package: wnpp Severity: wishlist Subject: ITP: r-cran-circular -- GNU R Circular Statistics Package: wnpp Owner: Shayan Doust Severity: wishlist * Package name: r-cran-circular Version : 0.4 Upstream Author : Ulric Lund , * URL : https://cran.r-project.org/package=circular * License : GPL-2 Programming Lang: GNU R Description : GNU R Circular Statistics Circular Statistics, from "Topics in circular Statistics" (2001) S. Rao Jammalamadaka and A. SenGupta, World Scientific. Remark: This package is maintained by Debian R Packages Maintainers at https://salsa.debian.org/r-pkg-team/r-cran-circular
Bug#970452: ITP: argh -- C++ header-only command line processing library
Package: wnpp Severity: wishlist Subject: ITP: argh -- C++ header-only command line processing library Package: wnpp Owner: Shayan Doust Severity: wishlist * Package name: argh Version : 1.3.1+ds Upstream Author : Adi Shavit * URL : https://github.com/adishavit/argh * License : BSD-3-Clause Programming Lang: C Description : C++ header-only command line processing library So many different command line processing libraries out there and none of them just work! Some bring their whole extended family of related and unrelated external dependencies (yes, I'm looking at you Boost). Some require quirky syntax and/or very verbose setups that sacrifice simplicity for the generation of a cute usage message and validation. Many come to dominate your main() file and yet others do not build on multiple plaforms - for some even their own tests and trivial usage cause crashes on some systems. Argh! . If you're writing a highly-sophisticated command line tool, then Boost.Program_options and its kind might give you many advanced options. However, if you need to get up and running quickly, effectively and with minimal fuss, give the single header-file argh a try. Remark: This package is maintained by Debian Med Packaging Team at https://salsa.debian.org/med-team/argh
Bug#970389: ITP: r-cran-textdata -- GNU R Download and Load Various Text Datasets
Package: wnpp Severity: wishlist Subject: ITP: r-cran-textdata -- GNU R Download and Load Various Text Datasets Package: wnpp Owner: Shayan Doust Severity: wishlist * Package name: r-cran-textdata Version : 0.4.1 Upstream Author : Emil Hvitfeldt , * URL : https://cran.r-project.org/package=textdata * License : MIT Programming Lang: GNU R Description : GNU R Download and Load Various Text Datasets Provides a framework to download, parse, and store text datasets on the disk and load them when needed. Includes various sentiment lexicons and labeled text data sets for classification and analysis. Remark: This package is maintained by Debian R Packages Maintainers at https://salsa.debian.org/r-pkg-team/r-cran-textdata
Bug#969639: ITP: r-cran-poissonbinomial -- GNU R Efficient Computation of Ordinary and Generalized Poisson
Package: wnpp Severity: wishlist Subject: ITP: r-cran-poissonbinomial -- GNU R Efficient Computation of Ordinary and Generalized Poisson Package: wnpp Owner: Shayan Doust Severity: wishlist * Package name: r-cran-poissonbinomial Version : 1.1.2 Upstream Author : Copyright: Florian Junge * URL : https://cran.r-project.org/package=PoissonBinomial * License : GPL-2+ Programming Lang: GNU R Description : GNU R Efficient Computation of Ordinary and Generalized Poisson Binomial Distributions Efficient implementations of multiple exact and approximate methods as described in Hong (2013) , Biscarri, Zhao & Brunner (2018) and Zhang, Hong & Balakrishnan (2018) for computing the probability mass, cumulative distribution and quantile functions, as well as generating random numbers for both the ordinary and generalized Poisson binomial distribution. Remark: This package is maintained by Debian R Packages Maintainers at https://salsa.debian.org/r-pkg-team/r-cran-poissonbinomial
Bug#968716: ITP: shasta -- nanopore whole genome assembly (binaries and scripts)
Package: wnpp Severity: wishlist Subject: ITP: shasta -- nanopore whole genome assembly (binaries and scripts) Package: wnpp Owner: Shayan Doust Severity: wishlist * Package name: shasta Version : 0.5.1 Upstream Author : Chan Zuckerberg Initiative * URL : https://github.com/chanzuckerberg/shasta * License : Expat Programming Lang: C++ Description : nanopore whole genome assembly (binaries and scripts) De novo assembly from Oxford Nanopore reads. The goal of the Shasta long read assembler is to rapidly produce accurate assembled sequence using as input DNA reads generated by Oxford Nanopore flow cells. . Computational methods used by the Shasta assembler include: . * Using a run-length representation of the read sequence. This makes the assembly process more resilient to errors in homopolymer repeat counts, which are the most common type of errors in Oxford Nanopore reads. . * Using in some phases of the computation a representation of the read sequence based on markers, a fixed subset of short k-mers (k ≈ 10). . Shasta assembly quality is comparable or better than assembly quality achieved by other long read assemblers. . This package contains the executable binaries (tools) and accommodating scripts. Remark: This package is maintained by Debian Med Packaging Team at https://salsa.debian.org/med-team/shasta
Bug#968565: ITP: r-cran-cmstatr -- GNU R Statistical Methods for Composite Material Data
Package: wnpp Severity: wishlist Subject: ITP: r-cran-cmstatr -- GNU R Statistical Methods for Composite Material Data Package: wnpp Owner: Shayan Doust Severity: wishlist * Package name: r-cran-cmstatr Version : 0.7.0 Upstream Author : Stefan Kloppenborg , * URL : https://cran.r-project.org/package=cmstatr * License : AGPL-3 Programming Lang: GNU R Description : GNU R Statistical Methods for Composite Material Data An implementation of the statistical methods commonly used for advanced composite materials in aerospace applications. This package focuses on calculating basis values (lower tolerance bounds) for material strength properties, as well as performing the associated diagnostic tests. This package provides functions for calculating basis values assuming several different distributions, as well as providing functions for non-parametric methods of computing basis values. Functions are also provided for testing the hypothesis that there is no difference between strength and modulus data from an alternate sample and that from a "qualification" or "baseline" sample. For a discussion of these statistical methods and their use, see the Composite Materials Handbook, Volume 1 (2012, ISBN: 978-0-7680-7811-4). Additional details about this package are available in the paper by Kloppenborg (2020, ). Remark: This package is maintained by Debian R Packages Maintainers at https://salsa.debian.org/r-pkg-team/r-cran-cmstatr
Bug#968191: ITP: damapper -- long read to reference genome mapping tool
Package: wnpp Severity: wishlist Subject: ITP: damapper -- long read to reference genome mapping tool Package: wnpp Owner: Shayan Doust Severity: wishlist * Package name: damapper Version : 0.0+git20200322.b2c9d7f Upstream Author : Dr. Eugene W. Myers * URL : https://github.com/thegenemyers/DAMAPPER * License : BSD-3-Clause Programming Lang: C Description : long read to reference genome mapping tool Recognised as the Damapper Library, this is a long read to reference genome mapping command line tool. Remark: This package is maintained by Debian Med Packaging Team at https://salsa.debian.org/med-team/damapper
Bug#966559: ITP: r-cran-ksamples -- GNU R K-Sample Rank Tests and their Combinations
Package: wnpp Severity: wishlist Subject: ITP: r-cran-ksamples -- GNU R K-Sample Rank Tests and their Combinations Package: wnpp Owner: Shayan Doust Severity: wishlist * Package name: r-cran-ksamples Version : 1.2 Upstream Author : Fritz Scholz * URL : https://cran.r-project.org/package=kSamples * License : GPL-2+ Programming Lang: GNU R Description : GNU R K-Sample Rank Tests and their Combinations Compares k samples using the Anderson-Darling test, Kruskal-Wallis type tests with different rank score criteria, Steel's multiple comparison test, and the Jonckheere-Terpstra (JT) test. It computes asymptotic, simulated or (limited) exact P-values, all valid under randomization, with or without ties, or conditionally under random sampling from populations, given the observed tie pattern. Except for Steel's test and the JT test it also combines these tests across several blocks of samples. Also analyzed are 2 x t contingency tables and their blocked combinations using the Kruskal-Wallis criterion. Steel's test is inverted to provide simultaneous confidence bounds for shift parameters. A plotting function compares tail probabilities obtained under asymptotic approximation with those obtained via simulation or exact calculations. Remark: This package is maintained by Debian R Packages Maintainers at https://salsa.debian.org/r-pkg-team/r-cran-ksamples
Bug#966558: ITP: fast5-research -- command line executable tools for python3-fast5-research
Package: wnpp Severity: wishlist Subject: ITP: fast5-research -- command line executable tools for python3-fast5-research Package: wnpp Owner: Shayan Doust Severity: wishlist * Package name: fast5-research Version : 1.2.21 Upstream Author : Oxford Nanopore Technologies Ltd. * URL : https://github.com/nanoporetech/fast5_research * License : MPL-2.0 Programming Lang: Python Description : command line executable tools for python3-fast5-research Python fast5 reading and writing functionality provided by ONT Research. This package comprises an API to HDF containers used by the research groups within Oxford Nanopore Technologies. It complements the official API. Reading and writing of read files can be accomplished as well as reading of bulk .fast5 files. It reads interface bulk .fast5 files for extracting reads, channel states, voltage, etcetera. . This package contains the executables and command line tools for python3-fast5-research. Remark: This package is maintained by Debian Med Packaging Team at https://salsa.debian.org/med-team/fast5-research
Bug#966267: ITP: google-auth-oauthlib -- oauthlib integration with google-auth
Package: wnpp Severity: wishlist Subject: ITP: google-auth-oauthlib -- oauthlib integration with google-auth Package: wnpp Owner: Shayan Doust Severity: wishlist * Package name: google-auth-oauthlib Version : 0.4.1 Upstream Author : , 2016, 2017, 2019 Google Inc. * URL : https://pypi.org/project/google-auth-oauthlib/ * License : Apache-2.0 Programming Lang: Python Description : oauthlib integration with google-auth This library provides oauthlib integration for use with google-auth. Remark: This package is maintained by Debian Python Modules Team at https://salsa.debian.org/python-team/modules/google-auth-oauthlib
Bug#966266: ITP: r-cran-suppdists -- GNU R Supplementary Distributions
Package: wnpp Severity: wishlist Subject: ITP: r-cran-suppdists -- GNU R Supplementary Distributions Package: wnpp Owner: Shayan Doust Severity: wishlist * Package name: r-cran-suppdists Version : 1.1 Upstream Author : Bob Wheeler, * URL : https://cran.r-project.org/package=SuppDists * License : GPL-2+ Programming Lang: GNU R Description : GNU R Supplementary Distributions Ten distributions supplementing those built into R. Inverse Gauss, Kruskal-Wallis, Kendall's Tau, Friedman's chi squared, Spearman's rho, maximum F ratio, the Pearson product moment correlation coefficient, Johnson distributions, normal scores and generalized hypergeometric distributions. Remark: This package is maintained by Debian R Packages Maintainers at https://salsa.debian.org/r-pkg-team/r-cran-suppdists
Bug#966204: ITP: relacy -- meticulous synchronization algorithm verifier for relaxed memory models
Package: wnpp Severity: wishlist Subject: ITP: relacy -- meticulous synchronization algorithm verifier for relaxed memory models Package: wnpp Owner: Shayan Doust Severity: wishlist * Package name: relacy Version : 0.0+git20191025.acc09bb Upstream Author : Dmitry S. Vyukov * URL : https://github.com/dvyukov/relacy * License : BSD-3-Clause Programming Lang: C Description : meticulous synchronization algorithm verifier for relaxed memory models Relacy Race Detector is a tool for efficient execution of unit tests for synchronization algorithms written in C++0x. Every user thread is represented as a fiber (ucontext). Every time only one fiber is running, and special scheduler controls interleaving between fibers. With random scheduler it just executes numerous amount of various interleavings between threads. With full search scheduler or context-bound scheduler it systematically executes all possible interleavings between threads. While executing particular interleaving it makes exhaustive verification of various aspects of execution (races, accesses to freed memory etc). . If no errors found then verification terminates when particular number of interleavings are verified (for random scheduler), or when all possible interleavings are verified (for full search scheduler). If error is found then tool outputs execution history which leads to error and terminates. Physically Relacy Race Detector is a header-only library for C++98. Remark: This package is maintained by Debian Med Packaging Team at https://salsa.debian.org/med-team/relacy
Bug#965226: ITP: r-cran-dslabs -- Data Science Labs
Package: wnpp Severity: wishlist Subject: ITP: r-cran-dslabs -- Data Science Labs Package: wnpp Owner: Shayan Doust Severity: wishlist * Package name: r-cran-dslabs Version : 0.7.3 Upstream Author : Rafael A. Irizarry * URL : https://cran.r-project.org/package=dslabs * License : Artistic-2.0 Programming Lang: GNU R Description : Data Science Labs Datasets and functions that can be used for data analysis practice, homework and projects in data science courses and workshops. 26 datasets are available for case studies in data visualization, statistical inference, modeling, linear regression, data wrangling and machine learning. Remark: This package is maintained by Debian R Packages Maintainers at https://salsa.debian.org/r-pkg-team/r-cran-dslabs
Bug#965079: ITP: graphbin -- refined binning of metagenomic contigs using assembly graphs
Package: wnpp Severity: wishlist Subject: ITP: graphbin -- refined binning of metagenomic contigs using assembly graphs Package: wnpp Owner: Shayan Doust Severity: wishlist * Package name: graphbin Version : 1.1 Upstream Author : Graphbin Project * URL : https://github.com/Vini2/GraphBin * License : GPL-2.0+ Programming Lang: Python Description : refined binning of metagenomic contigs using assembly graphs GraphBin is a NGS data-based metagenomic contig bin refinment tool that makes use of the contig connectivity information from the assembly graph to bin contigs. It utilizes the binning result of an existing binning tool and a label propagation algorithm to correct mis-binned contigs and predict the labels of contigs which are discarded due to short length. Remark: This package is maintained by Debian Med Packaging Team at https://salsa.debian.org/med-team/graphbin
Bug#964976: ITP: tao-config -- C++ header-only library that reads config files and produces a JSON value
Package: wnpp Severity: wishlist Subject: ITP: tao-config -- C++ header-only library that reads config files and produces a JSON value Package: wnpp Owner: Shayan Doust Severity: wishlist * Package name: tao-config Version : 0.0+git20200604.84a7383 Upstream Author : Dr. Colin Hirsch * URL : https://github.com/taocpp/config * License : Expat Programming Lang: C Description : C++ header-only library that reads config files and produces a JSON value C++ header-only library that reads config files based on JSON and JAXN formats and in turn, produces a single JSON valur as a result. . Its features are as follows: 1. JAXN syntax with extensions (backwards compatible with JSON). 2. JAXN data model (JSON extended with binary data and non-finites). 3. Meta data, all sub-values are annotated with filename and position. 4. Copy, reference, replace and delete anything in the JSON structure. 5. Multiple ways to read and parse other config and data files. 6. Uses environmental variables and the output of arbitrary shell commands. Remark: This package is maintained by Debian Med Packaging Team at https://salsa.debian.org/med-team/tao-config
Bug#964801: ITP: gneiss -- data analysis and visualisation toolbox for high dimensional proportions
Package: wnpp Severity: wishlist Subject: ITP: gneiss -- data analysis and visualisation toolbox for high dimensional proportions Package: wnpp Owner: Shayan Doust Severity: wishlist * Package name: gneiss Version : 0.4.6 Upstream Author : gneiss development team * URL : https://github.com/biocore/gneiss * License : BSD-3-Clause Programming Lang: Python Description : data analysis and visualisation toolbox for high dimensional proportions Canonically pronounced as 'nice', gneiss is a compositional data analysis and visualisation toolbox designed for analysing high dimensional proportions. Remark: This package is maintained by Debian Med Packaging Team at https://salsa.debian.org/med-team/gneiss
Bug#756017: Partial packaging
Hello Diane et. al., I am packaging gneiss[1], where one of its dependency is Bokeh. What is the progress of Bokeh at this time? Additionally, is this a WIP? Kind regards, Shayan Doust [1]: https://salsa.debian.org/med-team/gneiss On Sat, 14 Sep 2019 00:22:04 +0200 Pierre-Elliott =?utf-8?B?QsOpY3Vl?= wrote: > Le mardi 08 septembre 2015 à 22:25:11-0700, Diane Trout a écrit : > > I have a packaging tree that I'm using at: > > https://github.com/detrout/python-bokeh > > > > It can't be released to Debian until we find a solution for building > > BokehJS. > > (And that it also needs a jquery 2.1.1). > > > > But at least its a start. > > Dear Diane, > > It seems that bokeh 1.3.4 ships a version of BokehJS that is > non-minified and ready-to-use. Wouldn't that be a correct solution for > an initial packaging, even though one could wish to finish the proper > javascript package in a second time? > > With best regards, > > -- > Pierre-Elliott Bécue > GPG: 9AE0 4D98 6400 E3B6 7528 F493 0D44 2664 1949 74E2 > It's far easier to fight for one's principles than to live up to them. 0x6D7D441919D02395.asc Description: application/pgp-keys signature.asc Description: OpenPGP digital signature
Bug#964392: ITP: tao-json -- multifunctional and zero-dependency C++ header-only JSON library
Package: wnpp Severity: wishlist Subject: ITP: tao-json -- multifunctional and zero-dependency C++ header-only JSON library Package: wnpp Owner: Shayan Doust Severity: wishlist * Package name: tao-json Version : 1.0.0~beta.11 Upstream Author : Dr. Colin Hirsch * URL : https://github.com/taocpp/json * License : Expat Programming Lang: C++ Description : multifunctional and zero-dependency C++ header-only JSON library taoJSON is a zero-dependency C++ header-only JSON library that provides a generic Value Class, uses Type Traits to interoperate with C++ types, uses an Events Interface to convert to and from JSON, JAXN, CBOR, MsgPack and UBJSON, and much, much more. Remark: This package is maintained by Debian Med Packaging Team at https://salsa.debian.org/med-team/tao-json
Bug#964202: ITP: mecat2 -- ultra-fast and accurate de novo assembly tools for SMRT reads
Package: wnpp Severity: wishlist Subject: ITP: mecat2 -- ultra-fast and accurate de novo assembly tools for SMRT reads Package: wnpp Owner: Shayan Doust Severity: wishlist * Package name: mecat2 Version : 0.0+git20200428.f54c542 Upstream Author : Chuan-Le Xiao * URL : https://github.com/xiaochuanle/MECAT2 * License : GPL-3 Programming Lang: C Description : ultra-fast and accurate de novo assembly tools for SMRT reads An improved version of MECAT. It is an ultra-fast and accurate mapping and error correcting de novo assembly tools for single molecula sequencing (SMRT) reads. MECAT2 consists of the following three modules: 1. mecat2map: a fast and accurate alignment tool for SMRT reads. 2. mecat2cns: correct noisy reads based on their pairwise overlaps. 3. fsa: a string graph based assembly tool. Remark: This package is maintained by Debian Med Packaging Team at https://salsa.debian.org/med-team/mecat2
Bug#963981: ITP: dextractor -- (d)extractor and compression command library
Package: wnpp Severity: wishlist Subject: ITP: dextractor -- (d)extractor and compression command library Package: wnpp Owner: Shayan Doust Severity: wishlist * Package name: dextractor Version : 1.0 Upstream Author : Dr. Eugene W. Myers (EWM) * URL : https://github.com/thegenemyers/DEXTRACTOR * License : BSD-3-Clause Programming Lang: C Description : (d)extractor and compression command library Dextractor commands allow one to pull exactly and only the information needed for assembly and reconstruction from the source HDF5 files produced by the PacBio RS II sequencer, or from the source BAM files produced by the PacBio Sequel sequencer. . For each of the three extracted file types -- fasta, quiva, and arrow -- the library contains commands to compress the given file type, and to decompress it, which is a reversible process delivering the original uncompressed file. The compressed .fasta files, with the extension .dexta, consume 1/4 byte per base. The compressed .quiva files, with the extension .dexqv, consume 1.5 bytes per base on average, and the compressed .arrow files, with the extension .dexar, consume 1/4 byte per base . For more information, please view the available documentation at https://github.com/thegenemyers/DEXTRACTOR Remark: This package is maintained by Debian Med Packaging Team at https://salsa.debian.org/med-team/dextractor
Bug#963565: ITP: marginphase -- simultaneous haplotyping and genotyping
Package: wnpp Severity: wishlist Subject: ITP: marginphase -- simultaneous haplotyping and genotyping Package: wnpp Owner: Shayan Doust Severity: wishlist * Package name: marginphase Version : 0.0+git20181109.cdf139e Upstream Author : Benedict Paten * URL : https://github.com/benedictpaten/marginPhase * License : Expat Programming Lang: C Description : simultaneous haplotyping and genotyping MarginPhase is a program for simultaneous haplotyping and genotyping. Remark: This package is maintained by Debian Med Packaging Team at https://salsa.debian.org/med-team/marginphase
Bug#963218: ITP: libpll-2 -- Phylogenetic Likelihood Library 2
Package: wnpp Severity: wishlist Subject: ITP: libpll-2 -- Phylogenetic Likelihood Library 2 Package: wnpp Owner: Shayan Doust Severity: wishlist * Package name: libpll-2 Version : 0.3.2 Upstream Author : Tomas Flouri * URL : https://github.com/xflouris/libpll-2 * License : AGPL-3+ Programming Lang: C Description : Phylogenetic Likelihood Library 2 PLL is a highly optimised, parallelised software library to ease the development of new software tools dealing with phylogenetic inference. . Among the function included in PLL are parsing multiple sequence alignments (MSA) from PHYLIP and FASTA files, reading Newick trees, performing topological moves such as SPR and NNI, model optimisation, likelihood evaluation and partitioned analysis by assigning different substitution models to each partition of the MSA. PLL fully implements the GTR nucleotide substitution model for DNA data and a number of models for aminoacid data. . libpll-2 is the new official fork of libpll. It implements site repeats to speed up computations. . This package contains the dynamic library. Remark: This package is maintained by Debian Med Packaging Team at https://salsa.debian.org/med-team/libpll-2
Bug#963160: ITP: intake -- lightweight package for finding and investigating data
Package: wnpp Severity: wishlist Subject: ITP: intake -- lightweight package for finding and investigating data Package: wnpp Owner: Shayan Doust Severity: wishlist * Package name: intake Version : 0.6.0 Upstream Author : Anaconda Inc., Intake contributors * URL : https://github.com/intake/intake * License : BSD-2-clause Programming Lang: Python Description : lightweight package for finding and investigating data Intake is a leightweight set of tools for loading and sharing data in data science projects. Intake helps you: 1. Load data from a variety of formats into containers you already know, like Pandas dataframes, Python lists, NumPy arrays and more. 2. Convert boilerplate data loading code into reusable intake plugins. 3. Describe data sets in catalog files for easy reuse and sharing between projects and with others. 4. Share catalog information (and data sets) over the network with the Intake server. Remark: This package is maintained by Debian Med Packaging Team at https://salsa.debian.org/med-team/intake
Bug#962977: ITP: nanofilt -- filtering and trimming of long read sequencing data
Package: wnpp Severity: wishlist Subject: ITP: nanofilt -- filtering and trimming of long read sequencing data Package: wnpp Owner: Shayan Doust Severity: wishlist * Package name: nanofilt Version : 2.6.0 Upstream Author : Wouter De Coster * URL : https://github.com/wdecoster/nanofilt * License : GPL-3 Programming Lang: Python Description : filtering and trimming of long read sequencing data Filtering and trimming of long read sequencing data. Filtering on quality and/or read length, and optional trimming after passing filters. Reads from stdin, writes to stdout. Optionally reads directly from an uncompressed file specified on the command line. . Intended to be used: 1. directly after fastq extraction. 2. prior to mapping. 3. in a stream between extraction and mapping. Remark: This package is maintained by Debian Med Packaging Team at https://salsa.debian.org/med-team/nanofilt
Bug#962822: ITP: bmtk -- development package for building, simulating and analysing large-scale networks
Package: wnpp Severity: wishlist Subject: ITP: bmtk -- development package for building, simulating and analysing large-scale networks Package: wnpp Owner: Shayan Doust Severity: wishlist * Package name: bmtk Version : 0.0.7 Upstream Author : Allen Institute * URL : https://github.com/AllenInstitute/bmtk * License : BSD-3-Clause Programming Lang: Python Description : development package for building, simulating and analysing large-scale networks The brain modelling toolkit is a software development package for building, simulating and analysing large-scale networks of different levels of resolution. Remark: This package is maintained by Debian Med Packaging Team at https://salsa.debian.org/med-team/bmtk
Bug#962544: ITP: enlighten -- a console progress bar module for Python3
Package: wnpp Severity: wishlist Subject: ITP: enlighten -- a console progress bar module for Python3 Package: wnpp Owner: Shayan Doust Severity: wishlist * Package name: enlighten Version : 1.5.2 Upstream Author : , Avram Lubkin * URL : https://github.com/Rockhopper-Technologies/enlighten * License : MPL-2.0 Programming Lang: Python Description : a console progress bar module for Python3 Enlighten progress bar is a console progress bar module for Python3 which allows writing for stdout and stderr without any redirection. Remark: This package is maintained by Debian Med Packaging Team at https://salsa.debian.org/med-team/enlighten
Bug#962417: ITP: pll-modules -- high level modules for the low level phylogenetic likelihood library (devel)
Package: wnpp Severity: wishlist Subject: ITP: pll-modules -- high level modules for the low level phylogenetic likelihood library (devel) Package: wnpp Owner: Shayan Doust Severity: wishlist * Package name: pll-modules Version : 0.0+git20170809.d6cc565 Upstream Author : , 2016, Diego Darriba * URL : https://github.com/ddarriba/pll-modules * License : AGPL-3+ Programming Lang: C Description : high level modules for the low level phylogenetic likelihood library (devel) This package provides high level modules for the low level phylogenetic likelihood library. . This package contains the static library and header files. Remark: This package is maintained by Debian Med Packaging Team at https://salsa.debian.org/med-team/pll-modules
Bug#962057: ITP: covtobed -- convert the coverage track from a BAM file into a BED file
Package: wnpp Severity: wishlist Subject: ITP: covtobed -- convert the coverage track from a BAM file into a BED file Package: wnpp Owner: Shayan Doust Severity: wishlist * Package name: covtobed Version : 1.1.2 Upstream Author : Giovanni Birolo and Andrea Telatin * URL : https://github.com/telatin/covtobed * License : Expat Programming Lang: C Description : convert the coverage track from a BAM file into a BED file Reads one (or more) alignment files (sorted BAM) and prints a BED with the coverage. It will join consecutive bases with the same coverage, and can be used to only print a BED file with the regions having a specific coverage range. Remark: This package is maintained by Debian Med Packaging Team at https://salsa.debian.org/med-team/covtobed
Bug#944029: ITP: megahit -- ultra-fast and memory-efficient meta-genome assembler
Package: wnpp Severity: wishlist Subject: ITP: megahit -- ultra-fast and memory-efficient meta-genome assembler Package: wnpp Owner: Shayan Doust Severity: wishlist * Package name: megahit Version : 1.2.9 Upstream Author : The University of Hong Kong & L3 Bioinformatics Limited * URL : https://github.com/voutcn/megahit * License : GPL-3 Programming Lang: C Description : ultra-fast and memory-efficient meta-genome assembler Megahit is an ultra-fast and memory-efficient NGS assembler. It is optimized for metagenomes, but also works well on generic single genome assembly (small or mammalian size) and single-cell assembly. Remark: This package is maintained by Debian Med Packaging Team at https://salsa.debian.org/med-team/megahit
Bug#941280: ITP: bcalm -- de Bruijn compaction in low memory
Package: wnpp Severity: wishlist Subject: ITP: bcalm -- de Bruijn compaction in low memory Package: wnpp Owner: Shayan Doust Severity: wishlist * Package name: bcalm Version : 2.2.1 Upstream Author : INRIA <https://inria.fr/> * URL : https://github.com/GATB/bcalm * License : Expat Programming Lang: C Description : de Bruijn compaction in low memory A bioinformatics tool for constructing the compacted de Bruijn graph from sequencing data. . This is the parallel version of the BCALM software using gatb-core library. Remark: This package is maintained by Debian Med Packaging Team at https://salsa.debian.org/med-team/bcalm
Bug#940559: ITP: simka -- comparative metagenomics method dedicated to NGS datasets
Package: wnpp Severity: wishlist Subject: ITP: simka -- comparative metagenomics method dedicated to NGS datasets Package: wnpp Owner: Shayan Doust Severity: wishlist * Package name: simka Version : 1.5.1 Upstream Author : Inria * URL : https://github.com/GATB/simka * License : AGPL-3 Programming Lang: C Description : comparative metagenomics method dedicated to NGS datasets Simka is a de novo comparative metagenomics tool. Simka represents each dataset as a k-mer spectrum and compute several classical ecological distances between them. Remark: This package is maintained by Debian Med Packaging Team at https://salsa.debian.org/med-team/simka
Bug#933235: ITP: fast -- framework for Heterogeneous Medical Image Computing
Package: wnpp Severity: wishlist Subject: ITP: fast -- framework for Heterogeneous Medical Image Computing Package: wnpp Owner: Shayan Doust Severity: wishlist * Package name: fast Version : 3.0.0 Upstream Author : Norwegian University of Science and Technology * URL : https://github.com/smistad/FAST * License : BSD-2-Clause Programming Lang: C Description : framework for Heterogeneous Medical Image Computing An open-source cross-platform framework with the main goal of making it easier to do processing and visualization of medical images on heterogeneous systems (CPU+GPU). Has data streaming, deep learning, high- level data management, high-performance algorithms, interoperability with Insight Toolkit & integration with existing VTK / Qt applications as well as a fast concurrent visualization. Remark: This package is maintained by Debian Med Packaging Team at https://salsa.debian.org/med-team/fast
Bug#932369: ITP: mmseqs2 -- ultra fast and sensitive protein search and clustering.
Package: wnpp Severity: wishlist Subject: ITP: mmseqs2 -- ultra fast and sensitive protein search and clustering. Package: wnpp Owner: Shayan Doust Severity: wishlist * Package name: mmseqs2 Version : 9 Upstream Author : Söding Lab <https://mpibpc.mpg.de/soeding> * URL : https://github.com/soedinglab/MMseqs2 * License : GPLv3 Programming Lang: C Description : ultra fast and sensitive protein search and clustering. MMseqs2 (Many-against-Many sequence searching) is a software suite to search and cluster huge proteins/nucleotide sequence sets. MMseqs2 is open source GPL-licensed software implemented in C++ for Linux, MacOS, and (as beta version, via cygwin) Windows. The software is designed to run on multiple cores and servers and exhibits very good scalability. MMseqs2 can run 1 times faster than BLAST. At 100 times its speed it achieves almost the same sensitivity. It can perform profile searches with the same sensitivity as PSI-BLAST at over 400 times its speed. Remark: This package is maintained by Debian Med Packaging Team at https://salsa.debian.org/med-team/mmseqs2
Bug#931826: ITP: mindthegap -- Performs detection and assembly of DNA insertion variants in NGS read datasets.
Package: wnpp Severity: wishlist Subject: ITP: mindthegap -- Performs detection and assembly of DNA insertion variants in NGS read datasets. Package: wnpp Owner: Shayan Doust Severity: wishlist * Package name: mindthegap Version : 2.2.0 Upstream Author : GATB * URL : http://github.com/GATB/MindTheGap * License : AGPL-3 Programming Lang: C Description : Performs detection and assembly of DNA insertion variants in NGS read datasets. Designed to call insertions of any size, whether they are novel or duplicated, homozygous or heterozygous in the donor genome. It takes as input a set of reads and a reference genome. It outputs two sets of FASTA sequences: one is the set of breakpoints of detection insertion sites, the other is the set of assembled insertions for each breakpoint. MindTheGap can also be used as a genome assembly finishing tool. It can fill the gaps between a set of input contigs without any a priori on their relative order and orientation. It outputs the results in gfa file. Remark: This package is maintained by Debian Med Packaging Team at https://salsa.debian.org/med-team/mindthegap
