Bug#919748: ITP: nvchecker -- new-version checker for software releases

2019-01-18 Thread Afif Elghraoui
Package: wnpp Severity: wishlist Owner: Afif Elghraoui * Package name: nvchecker Version : 1.3 Upstream Author : lilydjwg * URL : https://github.com/lilydjwg/nvchecker * License : MIT Programming Lang: Python Description : new-version checker for

Bug#890220: ITP: assemblytics -- detect and analyze structural variants from a genome assembly

2018-02-11 Thread Afif Elghraoui
Package: wnpp Owner: Afif Elghraoui Severity: wishlist * Package name: assemblytics Version : 0~20170131 Upstream Author : Maria Nattestad * URL : http://assemblytics.com * License : MIT Programming Lang: Python, R Description : detect and analyze

Bug#889613: ITP: swiglpk -- Plain Python bindings for the GNU Linear Programming Kit

2018-02-04 Thread Afif Elghraoui
Package: wnpp Owner: Afif Elghraoui Severity: wishlist * Package name: swiglpk Version : 1.4.4 Upstream Author : The Novo Nordisk Foundation Center for Biosustainability * URL : https://github.com/biosustain/swiglpk * License : GPL Programming Lang: Python

Bug#889611: ITP: optlang -- sympy-based mathematical programming language

2018-02-04 Thread Afif Elghraoui
Package: wnpp Owner: Afif Elghraoui Severity: wishlist * Package name: optlang Version : 1.3.0 Upstream Author : Novo Nordisk Foundation Center for Biosustainability * URL : http://optlang.readthedocs.org/ * License : Apache Programming Lang: Python

Bug#878964: ITP: python-easydev -- common utilities to ease the development of Python packages

2017-10-17 Thread Afif Elghraoui
Package: wnpp Severity: wishlist Owner: Debian Med Team Control: block 878962 by -1 Control: block 878963 by -1 * Package name: python-easydev Version : 0.9.35 Upstream Author : Thomas Cokelaer * URL : https://easydev-python.readthedocs.io/en/latest/ * License

Bug#878963: ITP: python-colormap -- ease manipulation of matplotlib colormaps and color codecs

2017-10-17 Thread Afif Elghraoui
Package: wnpp Severity: wishlist Owner: Debian Med Team Control: block 878962 by -1 * Package name: python-colormap Version : 1.0.1 Upstream Author : Thomas Cokelaer * URL : https://colormap.readthedocs.io/ * License : BSD Programming Lang: Python Descripti

Bug#878962: ITP: hinge -- long read genome assembler based on hinging

2017-10-17 Thread Afif Elghraoui
Package: wnpp Severity: wishlist Owner: Debian Med Team * Package name: hinge Version : 0.5 Upstream Author : Govinda Kamath, Fei Xia, Ilan Shomorony, Thomas Courtade, and David Tse * URL :

Bug#805754: Processed: retitle to RFP: ensembl-tools -- Ensembl tools for genomic data processing

2017-03-04 Thread Afif Elghraoui
or a while. It involved packaging some other Ensembl APIs and seems to be difficult to keep up with. regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#855597: ITP: phyx -- phylogenetic analyses on trees and sequences for UNIX

2017-02-20 Thread Afif Elghraoui
Hi, Andreas, على الإثنين 20 شباط 2017 ‫08:26، كتب Andreas Tille: > Hi Afif > > On Mon, Feb 20, 2017 at 08:14:30AM -0800, Afif Elghraoui wrote: >> Description : phylogenetic analyses on trees and sequences for UNIX > > Please drop " for UNIX" here - sinc

Bug#855597: ITP: phyx -- phylogenetic analyses on trees and sequences for UNIX

2017-02-20 Thread Afif Elghraoui
Package: wnpp Severity: wishlist Owner: Debian Med Packaging Team * Package name: phyx Version : 0.99 Upstream Author : Joseph W. Brown, Joseph F. Walker, and Stephen A. Smith * URL : https://github.com/FePhyFoFum/phyx * License : GPL Programming Lang: C++

Bug#639910: ITP: simple-build-tool -- bootstrapping

2017-01-22 Thread Afif Elghraoui
compiler is necessary to otherwise avoid doing manual work. The alternative to bootstrapping a build tool is not manual work, but a different, maybe less efficient but still automatic approach. Thanks and regards Afif 1. http://git.savannah.gnu.org/cgit/make.git/tree/build.template -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#848122: ITP: pbcopper -- data structures, algorithms, and utilities for C++ applications

2016-12-14 Thread Afif Elghraoui
Package: wnpp Severity: wishlist Owner: Debian Med Packaging Team Control: block 847310 by -1 * Package name: pbcopper Version : 0.0.1 Upstream Author : Pacific Biosciences * URL : https://github.com/PacificBiosciences/pbcopper * License : BSD Programming La

Bug#847310: RFP: unanimity -- generate and process accurate genomic consensus sequences from single-molecule sequencing data

2016-12-07 Thread Afif Elghraoui
Package: wnpp Severity: wishlist * Package name: unanimity Version : 2.0.4 Upstream Author : Pacific Biosciences * URL : https://github.com/PacificBiosciences/unanimity * License : BSD Programming Lang: C++, Python Description : generate and process acc

Bug#841396: ITP: dascrubber -- alignment-based scrubbing pipeline for DNA sequencing reads

2016-10-20 Thread Afif Elghraoui
Package: wnpp Severity: wishlist Owner: Debian Med Packaging Team * Package name: dascrubber Version : 0~20160601 Upstream Author : Eugene W. Myers, Jr. * URL : https://github.com/thegenemyers/DASCRUBBER * License : BSD Programming Lang: C Description

Bug#832311: ITP: pbtestdata -- small Pacific Biosciences datasets for testing

2016-07-23 Thread Afif Elghraoui
Package: wnpp Severity: wishlist Owner: Debian Med Packaging Team * Package name: pbtestdata Version : 0.0.13 Upstream Author : Pacific Biosciences * URL : https://github.com/PacificBiosciences/PacBioTestData * License : BSD Programming Lang: Python Descri

Bug#829510: ITP: consensuscore2 -- generate consensus sequences for PacBio sequencing data

2016-07-03 Thread Afif Elghraoui
Package: wnpp Severity: wishlist Owner: Debian Med Packaging Team * Package name: consensuscore2 Version : 0.12.0 Upstream Author : Pacific Biosciences * URL : https://github.com/PacificBiosciences/ConsensusCore2 * License : BSD Programming Lang: C++, Python

Bug#829506: ITP: flask-multistatic -- A simple flask plugin for overriding static files

2016-07-03 Thread Afif Elghraoui
على الأحد 3 تـمـوز 2016 ‫15:15، كتب Sergio Durigan Junior: [...] > > This package is a dependency necessary for pagure. > Many thanks for working towards a pagure package! It looks like a very nice thing to have in Debian. regards Afif -- Afif Elghraoui | عفيف الغ

Bug#827638: ITP: sniffles -- structural variation caller using third-generation sequencing

2016-06-18 Thread Afif Elghraoui
Package: wnpp Severity: wishlist Owner: Afif Elghraoui * Package name: sniffles Version : 0.0.1 Upstream Author : Fritz Sedlazeck * URL : https://github.com/fritzsedlazeck/Sniffles * License : MIT Programming Lang: C++ Description : structural

Bug#811411: Maintainer upload is pending

2016-05-26 Thread Afif Elghraoui
Control: tag -1 + pending I'm planning to adopt this package and a maintainer upload is being prepared, pending translation updates. See the adduser-devel archives for May 2016 for more information. -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#811411: Joining the adduser Alioth team

2016-05-21 Thread Afif Elghraoui
ld like to publish that as part of the same project. Many thanks and regards Afif - -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name -BEGIN PGP SIGNATURE- Version: GnuPG v2 iQIcBAEBCAAGBQJXQMBOAAoJEFmyMG86+d3BzVgP/3bNXiumne+juA

Bug#822661: ITP: python-et-xmlfile -- low memory Python library for creating large XML files

2016-04-26 Thread Afif Elghraoui
Package: wnpp Severity: wishlist Owner: Afif Elghraoui Control: block 822414 by -1 * Package name: python-et-xmlfile Version : 1.0.1 Upstream Author : Charlie Clark and Elias Rabel * URL : https://bitbucket.org/openpyxl/et_xmlfile * License : MIT

Bug#820851: ITP: sprai -- single-pass sequencing read accuracy improver

2016-04-12 Thread Afif Elghraoui
Package: wnpp Severity: wishlist Owner: Debian Med Packaging Team * Package name: sprai Version : 0.9.9.12 Upstream Author : Takamasa Imai * URL : http://zombie.cb.k.u-tokyo.ac.jp/sprai/index.html * License : MIT Programming Lang: C, Perl, Python Descripti

Bug#818575: ITP: circlator -- circularize genome assemblies

2016-03-20 Thread Afif Elghraoui
Package: wnpp Severity: wishlist Owner: Debian Med Packaging Team * Package name: circlator Version : 1.2.0 Upstream Author : Martin Hunt & Nishadi De Silva * URL : http://sanger-pathogens.github.io/circlator/ * License : GPL Programming Lang: Python Descr

Bug#807802: pbsuite to move ahead without fringe dependency

2016-02-27 Thread Afif Elghraoui
https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=807804 -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#814867: contacting Debichem regarding inchi ITP

2016-02-23 Thread Afif Elghraoui
Hi, Have you already contacted the Debichem team about this ITP for inchi? Their mailing list is at . You'll probably want to talk to them about joining the team if you haven't already done so. Many thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#812175: RFS: qsopt-ex

2016-02-07 Thread Afif Elghraoui
http://anonscm.debian.org/cgit/debian-med/qsopt-ex.git Many thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#803542: trnascan-se_1.3.1+dfsg-1_amd64.changes REJECTED

2016-02-05 Thread Afif Elghraoui
Hello, على الأربعاء 3 شباط 2016 ‫23:40، كتب Andreas Tille: > Hi, > > On Wed, Feb 03, 2016 at 09:27:07PM -0800, Afif Elghraoui wrote: >>> there seems to be something wrong with this package. >>> A DFSG package should not be in non-free. >>> >> >

Bug#811154: poretools_0.5.1-1_amd64.changes REJECTED

2016-02-03 Thread Afif Elghraoui
ards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#803542: trnascan-se_1.3.1+dfsg-1_amd64.changes REJECTED

2016-02-03 Thread Afif Elghraoui
o you have a more appropriate alternative to +dfsg for the repack suffix? Thanks and regards Afif 1. https://lists.alioth.debian.org/pipermail/debian-med-packaging/2015-November/036574.html -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#811460: [Debian-med-packaging] Bug#811460: ITP: fast5 -- library for reading Oxford Nanopore Fast5 files

2016-01-25 Thread Afif Elghraoui
preciated :) I myself have mostly just been working with Pacific Biosciences data, but I thought Debian could get ahead and be prepared with software for analysis of nanopore data. Thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#812175: ITP: qsopt-ex -- exact linear and integer programming solver

2016-01-21 Thread Afif Elghraoui
, though. I generally like to copy the developers of the software on these messages to notify that the packaging is ongoing. Thanks for providing it under a free license. Many thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name على الخميس 21 كانون الثاني 2016 ‫05:19، كتب

Bug#812175: ITP: qsopt-ex -- exact linear and integer programming solver

2016-01-21 Thread Afif Elghraoui
Package: wnpp Severity: wishlist Owner: Debian Med Packaging Team * Package name: qsopt-ex Version : 2.5.10.3 Upstream Author : Daniel Espinoza and others; currently maintained by Jon Lund Steffenson * URL : http://www.dii.uchile.cl/~daespino/ESolver_doc/main.html *

Bug#811458: RFS: nanopolish

2016-01-20 Thread Afif Elghraoui
Hello, Since fast5 was accepted (Thanks for uploading it, Andreas), nanopolish is now ready to go in. Could someone please upload this one? git+ssh://git.debian.org/git/debian-med/nanopolish.git http://anonscm.debian.org/debian-med/nanopolish.git Many thanks and regards Afif -- Afif Elghraoui

Bug#811460: RFS: fast5

2016-01-19 Thread Afif Elghraoui
Hello, I finished the fast5 package, which is needed for nanopolish. Could someone please upload to unstable? git+ssh://git.debian.org/git/debian-med/fast5.git http://anonscm.debian.org/cgit/debian-med/fast5.git Many thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http

Bug#811460: ITP: fast5 -- library for reading Oxford Nanopore Fast5 files

2016-01-19 Thread Afif Elghraoui
Package: wnpp Severity: wishlist Owner: Debian Med Packaging Team Control: block 811458 by -1 * Package name: fast5 Version : 0~20150918 Upstream Author : Matei David * URL : https://github.com/mateidavid/fast5 * License : MIT Programming Lang: C++ Descript

Bug#811458: ITP: nanopolish -- consensus caller for nanopore sequencing data

2016-01-18 Thread Afif Elghraoui
Package: wnpp Severity: wishlist Owner: Debian Med Packaging Team * Package name: nanopolish Version : 0.4.0 Upstream Author : Jared Simpson * URL : https://github.com/jts/nanopolish * License : MIT Programming Lang: C++ Description : consensus caller

Bug#811154: RFS: poretools

2016-01-16 Thread Afif Elghraoui
Hi, team, I've completed the poretools package after forgetting about it for some time. Could someone please upload to unstable? git+ssh://git.debian.org/git/debian-med/poretools.git http://anonscm.debian.org/cgit/debian-med/poretools.git Many thanks and regards Afif -- Afif Elghraoui |

Bug#811154: ITP: poretools -- toolkit for nanopore nucleotide sequencing data

2016-01-15 Thread Afif Elghraoui
Package: wnpp Severity: wishlist Owner: Debian Med Packaging Team * Package name: poretools Version : 0.5.1 Upstream Author : Aaron Quinlan & Nick Loman * URL : http://poretools.readthedocs.org * License : GPL Programming Lang: Python Description : too

Bug#395843: wgs-assembler is now canu

2016-01-15 Thread Afif Elghraoui
hedocs.org/en/latest/ -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#810576: ITP: hail -- Efficiently extract arbitrary lines from a file or stream

2016-01-09 Thread Afif Elghraoui
Hi, Kevin, على السبت 9 كانون الثاني 2016 ‫15:17، كتب Kevin Murray: > Package: wnpp > Severity: wishlist > Owner: Kevin Murray > > * Package name: hail > Version : 0.1.1 > Upstream Author : Kevin Murray > * URL : https://github.com/kdmurray91/hail > * License

Bug#808895: ITP: lofreq -- sensitive variant calling from sequencing data

2015-12-23 Thread Afif Elghraoui
Package: wnpp Severity: wishlist Owner: Debian Med Packaging Team * Package name: lofreq Version : 2.1.2 Upstream Author : Andreas Wilm and Niranjan Nagarajan * URL : http://csb5.github.io/lofreq * License : MIT Programming Lang: C, Python Description

Bug#703256: [Pkg-gridengine-devel] moving the gridengine team repository to collab-maint

2015-12-23 Thread Afif Elghraoui
n access it. >> > Are you a Debian Maintainer and/or do you need sponsoring for uploads? > He said he would need sponsors, but I've offered to do so as well (in > case you want this off your hands). I am a DM, but the package in preparation adds new binary packages. Wouter k

Bug#703256: moving the gridengine team repository to collab-maint

2015-12-22 Thread Afif Elghraoui
rmail/pkg-gridengine-devel/2015-October/000774.html 4. https://lists.alioth.debian.org/pipermail/pkg-gridengine-devel/2015-October/000779.html -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name signature.asc Description: OpenPGP digital signature

Bug#808708: RFS: falconkit (blocker for wgs-assembler)

2015-12-21 Thread Afif Elghraoui
at git+ssh://git.debian.org/git/debian-med/falconkit.git and it's browsable at the following link, in case anyone would like to review: http://anonscm.debian.org/cgit/debian-med/falconkit.git Many thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#808708: ITP: falconkit -- genome assembly toolkit

2015-12-21 Thread Afif Elghraoui
Package: wnpp Severity: wishlist Owner: Debian Med Packaging Team Control: block 395843 by -1 * Package name: falconkit Version : 0.4.0 Upstream Author : Jason Chin * URL : https://github.com/PacificBiosciences/FALCON * License : BSD Programming Lang: Python

Bug#807804: status of packaging intervaltree

2015-12-19 Thread Afif Elghraoui
I'm waiting for the Python 3.5 compatibility issue [1] to be resolved before finalizing this package. 1. https://github.com/chaimleib/intervaltree/issues/35 -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#808202: RFS: pbbarcode

2015-12-18 Thread Afif Elghraoui
he package needs to be revised for acceptance to unstable, I would just delete/update the tag. Otherwise, I will surely forget until the next time I have to work on the package. Many thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#808202: ITP: pbbarcode -- annotate PacBio sequencing reads with barcode information

2015-12-17 Thread Afif Elghraoui
Package: wnpp Severity: wishlist Owner: Debian Med Packaging Team Control: block 787977 by -1 * Package name: pbbarcode Version : 0.8.0 Upstream Author : Pacific Biosciences * URL : https://github.com/PacificBiosciences/pbbarcode * License : BSD Programming

Bug#807804: ITP: python-intervaltree -- mutable, self-balancing interval tree

2015-12-13 Thread Afif Elghraoui
Package: wnpp Severity: wishlist Owner: Afif Elghraoui Control: block 807803 by -1 * Package name: python-intervaltree Version : 2.1.0 Upstream Author : Chaim-Leib Halbert * URL : https://github.com/chaimleib/intervaltree * License : Apache 2.0 Programming

Bug#807803: ITP: python-intervaltree-bio -- interval tree convenience classes for genomic data

2015-12-13 Thread Afif Elghraoui
Package: wnpp Severity: wishlist Owner: Debian Med Packaging Team Control: block 807802 by -1 * Package name: python-intervaltree-bio Version : 1.0.1 Upstream Author : Konstantin Tretyakov * URL : https://github.com/konstantint/intervaltree-bio * License : MIT

Bug#807802: ITP: pbsuite -- software for Pacific Biosciences sequencing data

2015-12-13 Thread Afif Elghraoui
Package: wnpp Severity: wishlist Owner: Debian Med Packaging Team Control: block -1 by 796644 * Package name: pbsuite Version : 15.8.24 Upstream Author : Adam English * URL : http://sourceforge.net/projects/pb-jelly * License : BSD Programming Lang: Python

Bug#796644: RFS: pbdagcon (unstable NEW)

2015-12-11 Thread Afif Elghraoui
Hi, team, I've completed the pbdagcon package. Could someone upload to unstable, please? The repository is at: git+ssh://git.debian.org/git/debian-med/pbdagcon.git http://anonscm.debian.org/cgit/debian-med/pbdagcon.git Many thanks for all your support! regards Afif -- Afif Elghraoui |

Bug#797676: RFS: kineticstools (unstable NEW)

2015-12-09 Thread Afif Elghraoui
Hi, team, I have the kineticstools package ready. Could someone upload to Unstable, please? The repository is at: git+ssh://git.debian.org/git/debian-med/kineticstools.git http://anonscm.debian.org/cgit/debian-med/kineticstools.git Many thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي

Bug#798218: pbseqlib_0~20151014+gitbe5d1bf-1_amd64.changes is NEW

2015-12-08 Thread Afif Elghraoui
which is in turn blocking still another package). I'm waiting for this one to be accepted before I can move on with that work. Many thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name على الأربعاء 18 تشرين الثاني 2015 ‫22:58، كتب Afif Elghraoui: > > The

Bug#803542: trnascan-se_1.3.1+dfsg-1_amd64.changes REJECTED

2015-11-26 Thread Afif Elghraoui
nt to do anything about it. May I suggest that we upload the package to non-free in the meantime? Thanks and regards Afif 1. https://github.com/groleo/mpatrol/blob/master/tools/dbmalloc.h 2. https://packages.qa.debian.org/m/mpatrol.html 3. http://c-faq.com/resources/mallocdbg.html -- Afif Elgh

Bug#798872: python-pbcommand_0.2.16-1_amd64.changes REJECTED

2015-11-22 Thread Afif Elghraoui
Hi, Charles, I've addressed the below issue in git. Would you be able to upload this again, please? Many thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name On الأحد 22 تشرين الثاني 2015 08:00, Thorsten Alteholz wrote: > > Hi Afif, > > please ad

Bug#805754: ITP: ensembl-tools -- Ensembl tools for genomic data processing

2015-11-21 Thread Afif Elghraoui
Package: wnpp Severity: wishlist Owner: Debian Med Packaging Team * Package name: ensembl-tools Version : 82 Upstream Author : European Bioinformatics Institute & Wellcome Trust Sanger Institute * URL : http://www.ensembl.org/info/docs/tools/index.html * License

Bug#805743: ITP: pyconfigure -- automatic configure script builder for Python software

2015-11-21 Thread Afif Elghraoui
Package: wnpp Severity: wishlist Owner: Afif Elghraoui * Package name: pyconfigure Version : 0.2.2 Upstream Author : Brandon Invergo * URL : https://www.gnu.org/software/pyconfigure/ * License : GPL Programming Lang: Python Description : automatic

Bug#805607: RFS: piler - genomic repeat discovery

2015-11-19 Thread Afif Elghraoui
-- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#805607: ITP: piler -- genomic repeat analysis

2015-11-19 Thread Afif Elghraoui
Package: wnpp Severity: wishlist Owner: Debian Med Packaging Team * Package name: piler Version : 0~20140707 Upstream Author : Robert Edgar * URL : http://www.drive5.com/piler/ * License : Public Domain Programming Lang: C, C++ Description : genomic rep

Bug#798218: RFS: pbseqlib (unstable)

2015-11-16 Thread Afif Elghraoui
ed/pbseqlib.git Since these libraries are for internal use by other programs, upstream has not put versions in the library sonames, but this should be alright given its intended use. Many thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#805230: RFS: python-pymummer (unstable)

2015-11-15 Thread Afif Elghraoui
Hi, team, I've finished the python-pymummer package. Would someone please upload to unstable? git+ssh://git.debian.org/git/debian-med/python-pymummer.git http://anonscm.debian.org/cgit/debian-med/python-pymummer.git Many thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي

Bug#805230: ITP: python-pymummer -- Python interface to MUMmer

2015-11-15 Thread Afif Elghraoui
Package: wnpp Severity: wishlist Owner: Debian Med Packaging Team * Package name: python-pymummer Version : 0.6.1 Upstream Author : 2015 Martin Hunt and Nishadi De Silva * URL : https://github.com/sanger-pathogens/pymummer * License : GPL Programming Lang:

Bug#804007: RFS: bcftools

2015-11-09 Thread Afif Elghraoui
Hi, team, I finished preparing the bcftools package: git+ssh://git.debian.org/git/debian-med/bcftools.git http://anonscm.debian.org/cgit/debian-med/bcftools.git Would someone upload to unstable, please? Many thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#804007: pre-existing git repository for bcftools

2015-11-03 Thread Afif Elghraoui
anew, would it be alright if I discard the old repository on Alioth? That attempt targets a much older upstream release. Thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#804007: ITP: bcftools -- utilities for genomic variant calling and manipulating VCF and BCF files

2015-11-03 Thread Afif Elghraoui
Package: wnpp Severity: wishlist Owner: Debian Med Packaging Team * Package name: bcftools Version : 1.2 Upstream Author : Petr Danecek, Shane McCarthy and John Marshall * URL : http://samtools.github.io/bcftools/ * License : GPL or MIT/X Programming Lang: C

Bug#803542: RFS: trnascan-se (NEW)

2015-11-01 Thread Afif Elghraoui
Hi, team, I've finished preparing a package for trnascan-se. Would someone please upload to unstable? git+ssh://git.debian.org/git/debian-med/trnascan-se.git http://anonscm.debian.org/cgit/debian-med/trnascan-se.git Many thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي

Bug#803542: ITP: trnascan-se -- detection of transfer RNA genes in genomic sequence

2015-10-31 Thread Afif Elghraoui
Package: wnpp Severity: wishlist Owner: Debian Med Packaging Team * Package name: trnascan-se Version : 1.3.1 Upstream Author : Todd Lowe and colleagues * URL : http://lowelab.ucsc.edu/tRNAscan-SE * License : GPL Programming Lang: C, Perl Description :

Bug#802739: artemis_16.0.0+dfsg-1_amd64.changes REJECTED

2015-10-27 Thread Afif Elghraoui
as, would you mind uploading again? The corrected version is in git now. Thanks, apologies, and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#798872: RFS: python-pbcommand (NEW)

2015-10-26 Thread Afif Elghraoui
gards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#802041: RFS: python-avro

2015-10-24 Thread Afif Elghraoui
o.git Would someone please upload to unstable? Many thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#802739: ITP: artemis -- genome browser and annotation tool

2015-10-22 Thread Afif Elghraoui
Package: wnpp Severity: wishlist Owner: Debian Med Packaging Team * Package name: artemis Version : 16.0.0 Upstream Author : Genome Research Limited * URL : http://www.sanger.ac.uk/resources/software/artemis * License : GPL Programming Lang: Java Descripti

Bug#802041: ITP: python-avro -- Python interface to Apache Avro data serialization system

2015-10-17 Thread Afif Elghraoui
Package: wnpp Severity: wishlist Owner: Debian Med Packaging Team Control: block 798872 by -1 * Package name: python-avro Version : 1.7.7 Upstream Author : Apache Software Foundation * URL : http://avro.apache.org * License : Apache 2.0 Programming Lang: Pyth

Bug#794447: RFS: pbgenomicconsensus (NEW)

2015-10-13 Thread Afif Elghraoui
Hi, team, I finished preparing pbgenomicconsensus. Could someone please upload to unstable? http://anonscm.debian.org/cgit/debian-med/pbgenomicconsensus.git/ ssh://git.debian.org/git/debian-med/pbgenomicconsensus.git Many thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http

Bug#795619: RFP: python-cylp (initial packaging available)

2015-09-20 Thread Afif Elghraoui
hon3-packaging), but obviously, Python2 packaging needs to be working first. Many thanks and regards Afif 1. http://bugs.debian.org/795619 -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#798873: ITP: dazzdb -- database library for the dazzler assembler

2015-09-13 Thread Afif Elghraoui
Package: wnpp Severity: wishlist Owner: Debian Med Packaging Team * Package name: dazzdb Version : 1.0 Upstream Author : Eugene W. Myers, Jr. * URL : https://github.com/thegenemyers/DAZZ_DB * License : BSD Programming Lang: C Description : database lib

Bug#798872: ITP: pbcommand -- common command-line interface for Pacific Biosciences analysis modules

2015-09-13 Thread Afif Elghraoui
Package: wnpp Severity: wishlist Owner: Debian Med Packaging Team Control: block 797676 by -1 * Package name: pbcommand Version : 0.2.8 Upstream Author : Pacific Biosciences * URL : https://github.com/PacificBiosciences/pbcommand * License : BSD Programming

Bug#797675: [Debian-med-packaging] Bug#797675: RFS: pbalign (NEW)

2015-09-07 Thread Afif Elghraoui
Hello, I've made the requested changes to pbalign. Could someone please sponsor? Thanks and regards Afif On الأحد 6 أيلول 2015 10:15, Afif Elghraoui wrote: > Hi, Andreas, > > On الأحد 6 أيلول 2015 06:27, Andreas Tille wrote: >> On Sun, Sep 06, 2015 at 02:13:12AM -0700,

Bug#798220: ITP: pbbam -- Pacific Biosciences binary alignment/map (BAM) library

2015-09-06 Thread Afif Elghraoui
Package: wnpp Severity: wishlist Owner: Debian Med Packaging Team * Package name: pbbam Version : 0.1.0 Upstream Author : Pacific Biosciences * URL : https://github.com/PacificBiosciences/pbbam * License : BSD Programming Lang: C++ Description : Pacifi

Bug#798218: ITP: pbseqlib -- libraries for analyzing Pacific Biosciences sequences

2015-09-06 Thread Afif Elghraoui
Package: wnpp Severity: wishlist Owner: Debian Med Packaging Control: affects -1 blasr * Package name: pbseqlib Version : 0~20150702+git98a302a Upstream Author : Pacific Biosciences * URL : https://github.com/PacificBiosciences/blasr_libcpp * License : BSD P

Bug#797675: RFS: pbalign (NEW)

2015-09-06 Thread Afif Elghraoui
h has also been renamed: git+ssh://git.debian.org/git/debian-med/pbalign.git Could someone sponsor this, please? Many thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#794450: RFS: python-pbconsensuscore (NEW)

2015-09-03 Thread Afif Elghraoui
Hi, all, I've completed preparation of the python-pbconsensuscore package. Could someone sponsor this upload, please? The repository is at git+ssh://git.debian.org/git/debian-med/python-pbconsensuscore.git Thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#797737: RFP: python-cram -- simple testing framework for command line applications

2015-09-02 Thread Afif Elghraoui
Package: wnpp Severity: wishlist Control: affects -1 blasr python-pbh5tools * Package name: python-cram Version : 0.6 Upstream Author : Brodie Rao * URL : https://github.com/brodie/cram * License : GPL Programming Lang: Python Description : simple testi

Bug#796644: [Debian-med-packaging] Bug#796644: Please push current state if there is some local Git

2015-09-01 Thread Afif Elghraoui
e for this effort. Thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#797676: ITP: python-kineticstools -- detecting DNA modifications from single molecule, real-time sequencing data

2015-09-01 Thread Afif Elghraoui
Package: wnpp Severity: wishlist Owner: Debian Med Packaging Team Control: block 787977 by -1 * Package name: python-kineticstools Version : 0.5.1 Upstream Author : Pacific Biosciences * URL : https://github.com/PacificBiosciences/kineticsTools * License : BSD

Bug#797352: ITP: daligner -- local alignment discovery between long nucleotide sequencing reads

2015-08-29 Thread Afif Elghraoui
Package: wnpp Severity: wishlist Owner: Debian Med Packaging Team * Package name: daligner Version : 1.0 Upstream Author : Eugene W. Myers, Jr. * URL : http://github.com/thegenemyers/DALIGNER * License : BSD Programming Lang: C Description : local alig

Bug#796640: [Debian-med-packaging] ITP: mhap -- locality-sensitive hashing to detect long-read overlaps

2015-08-28 Thread Afif Elghraoui
;t continue working on mhap until its build-dependency jaligner enters the archive. regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#796644: ITP: pbdagcon -- sequence consensus algorithm implementation based on directed acyclic graphs

2015-08-23 Thread Afif Elghraoui
Package: wnpp Severity: wishlist Owner: Debian Med Packaging Team Control: block 787977 by -1 * Package name: pbdagcon Version : git1d12e13 Upstream Author : Pacific Biosciences * URL : https://github.com/PacificBiosciences/pbdagcon * License : BSD** Program

Bug#796643: ITP: libuncommons-maths-java -- Random number generators, probability distributions, combinatorics and statistics for Java

2015-08-22 Thread Afif Elghraoui
Package: wnpp Severity: wishlist Owner: Debian Med Packaging Team Control: block 395843 by -1 * Package name: libuncommons-maths-java Version : 1.2.3 Upstream Author : Daniel W. Dyer * URL : http://maths.uncommons.org * License : Apache Programming Lang: Java

Bug#796640: ITP: mhap -- locality-sensitive hashing to detect long-read overlaps

2015-08-22 Thread Afif Elghraoui
Package: wnpp Severity: wishlist Owner: Debian Med Packaging Team Control: block 395843 by -1 * Package name: mhap Version : 1.6 Upstream Author : Sergey Koren , Konstantin Berlin * URL : https://github.com/marbl/MHAP * License : Apache Programming Lang: Ja

Bug#787982: python-pbh5tools ready to upload

2015-08-15 Thread Afif Elghraoui
Hi, all, I've finished preparing the first version of the pbh5tools package. Could someone upload to unstable please? Many thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#795619: RFP: python-cylp -- Python interface to COIN-OR linear and mixed-integer program solvers

2015-08-15 Thread Afif Elghraoui
Package: wnpp Severity: wishlist * Package name: python-cylp Version : 0.7.2 Upstream Author : Mehdi Towhidi * URL : https://github.com/coin-or/CyLP * License : CPL Programming Lang: Python Description : Python interface to COIN-OR linear and mixed-inte

Bug#794450: ITP: pb-consensuscore -- library of multiple nucleotide sequence consensus routines

2015-08-03 Thread Afif Elghraoui
Package: wnpp Severity: wishlist Owner: Debian Med Packaging Team Control: block 794447 by -1 * Package name: pb-consensuscore Version : 1.0.0 Upstream Author : Pacific Biosciences * URL : https://github.com/PacificBiosciences/ConsensusCore * License : BSD P

Bug#794447: ITP: pb-genomicconsensus -- Pacific Biosciences variant and consensus caller

2015-08-03 Thread Afif Elghraoui
Package: wnpp Severity: wishlist Owner: Debian Med Packaging Team Control: block 787977 by ! * Package name: pb-genomicconsensus Version : 1.0.0 Upstream Author : Pacific Biosciences * URL : https://github.com/PacificBiosciences/GenomicConsensus * License : BS

Bug#787977: Debian packages for the SMRTAnalysis suite (and Python3 compatibility)

2015-07-25 Thread Afif Elghraoui
_0~20150520%2B2004-1.html 4. https://wiki.debian.org/Python/StretchRoadmap 5. https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=783833#10 6. http://anonscm.debian.org/cgit/debian-med/python-pbcore.git/tree/debian/patches/modernize-python.patch -- Afif Elghraoui | عفيف الغراوي http://afif.g

Bug#792664: ITP: ori -- secure distributed file system

2015-07-17 Thread Afif Elghraoui
I would very much like to have orifs on my android phone. > It looks like this is a direction the developers intend to go [2]. 1. https://mailman.stanford.edu/pipermail/orifs-devel/2015-June/000171.html 2. https://mailman.stanford.edu/pipermail/orifs-devel/2015-April/000163.html Reg

Bug#792664: ITP: ori -- secure distributed file system

2015-07-17 Thread Afif Elghraoui
Package: wnpp Severity: wishlist Owner: Afif Elghraoui X-Debbugs-Cc: debian-de...@lists.debian.org * Package name: ori Version : 0.8.1 Upstream Author : Stanford University * URL : http://ori.scs.stanford.edu/ * License : ori (MIT-like) Programming Lang: C

Bug#787981: Request for Sponsorship - python-pbcore

2015-06-28 Thread Afif Elghraoui
Hello, I have updated this package for python3 and it is lintian clean. Would someone be able to upload to experimental? Its dependency python-pysam currently resides there. Many thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name -- To UNSUBSCRIBE, email to

Bug#787981: Status of python-pbcore

2015-06-24 Thread Afif Elghraoui
possible. -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/558b7f85.4040...@ghraoui.name

Bug#787982: pbh5tools status

2015-06-21 Thread Afif Elghraoui
* This package build-depends on python-pbcore (#787981) * This package is python2-only and must be modified to support both python2 and python3. -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of

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