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

[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 software releases

 nvchecker (short for new version checker) is for checking if a new
 version of some software has been released.


This is a nice vendor-neutral solution for release monitoring. I think it
can also be quite useful in research, for example, to watch for updates of all
tools used in an analysis. And it doesn't have to be limited to watching
software releases, either. It could be applied to watching updates in
reference databases.

I intend to maintain nvchecker in the Debian group on salsa.

Afif

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

[Afif Elghraoui]

Package: wnpp
Owner: Afif Elghraoui <a...@debian.org>
Severity: wishlist

* Package name: assemblytics
  Version : 0~20170131
  Upstream Author : Maria Nattestad <mnatt...@cshl.edu>
* URL : http://assemblytics.com
* License : MIT
  Programming Lang: Python, R
  Description : detect and analyze structural variants from a genome
assembly

Assemblytics incorporates a unique anchor filtering approach to increase
robustness to repetitive elements, and identifies six classes of variants
based on their distinct alignment signatures. Assemblytics can be applied
both to comparing aberrant genomes, such as human cancers, to a reference,
or to identify differences between related species.

This will be maintained by Debian Med.

-- 
Afif Elghraoui | عفيف الغراوي
http://afif.ghraoui.name

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

[Afif Elghraoui]

Package: wnpp
Owner: Afif Elghraoui <a...@debian.org>
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
  Description : Plain Python bindings for the GNU Linear Programming Kit

swiglpk just provides plain SWIG bindings to the underlying C library
of the GNU Linear Programming Kit. It is not a high-level wrapper for GLPK.

This is a dependency of optlang and a new dependency of python-cobra. It
will be maintained by the Debian Science team.

-- 
Afif Elghraoui | عفيف الغراوي
http://afif.ghraoui.name

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

[Afif Elghraoui]

Package: wnpp
Owner: Afif Elghraoui <a...@debian.org>
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

  Description : sympy-based mathematical programming language

Optlang is a Python package for solving mathematical optimization
problems, i.e. maximizing or minimizing an objective function over a set
of variables subject to a number of constraints. Optlang provides a
common interface to a series of optimization tools, so different solver
backends can be changed in a transparent way. Optlang's object-oriented
API takes advantage of the symbolic math library sympy to allow
objective functions and constraints to be easily formulated from
symbolic expressions of variables (see examples).

This is a new dependency of python-cobra. It will be maintained under
Debian Science.

-- 
Afif Elghraoui | عفيف الغراوي
http://afif.ghraoui.name

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

[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 : BSD
  Programming Lang: Python
  Description : common utilities to ease the development of Python packages

 The package easydev provides miscellaneous functions that are often used in
 other Python packages. easydev should help developers in speeding up their
 own developments.

This is a dependency of hinge and python-colormap. It will be maintained by the 
Debian Med team.

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

[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
  Description : ease manipulation of matplotlib colormaps and color codecs

 The colormap package provides simple utilities to convert colors between RGB,
 HEX, HLS, HUV and a class to easily build colormaps for matplotlib. All
 matplotlib colormaps and some R colormaps are available altogether. The
 plot_colormap method (see below) is handy to quickly pick up a colormaps and
 the test_colormap is useful to see test a new colormap.

This is a dependency for hinge and so will be maintained by Debian Med as well.

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

[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 : https://github.com/HingeAssembler/HINGE
* License : BSD
  Programming Lang: C++, Python
  Description : long read genome assembler based on hinging

 HINGE is a genome assembler that seeks to achieve optimal repeat resolution
 by distinguishing repeats that can be resolved given the data from those that
 cannot. This is accomplished by adding “hinges” to reads for constructing an
 overlap graph where only unresolvable repeats are merged. As a result, HINGE
 combines the error resilience of overlap-based assemblers with
 repeat-resolution capabilities of de Bruijn graph assemblers.


This will be maintained by the Debian Med team.

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

[Afif Elghraoui]

Hi, Andreas,

على السبت  4 آذار 2017 ‫09:54، كتب Andreas Tille:
> Hi Afif,
> 
> you left an empty Git archive
> 
>git://git.debian.org/git/debian-med/ensembl-tools.git
> 
> Do you have any local repository with some preliminary work?  Not that I
> have any specific interest - but I wonder whether there is some stuff
> hanging around which could help once somebody might like to work on
> this.
> 

I did, but VEP (the tool I was interested in) was moved to a separate
upstream project. I am moving soon, so will not have a chance to push my
current work for 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

[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 - since this is redundant on a Debian system.
> May be
> 
>s/ for UNIX/ at command line enabling pipes/
> 
> or something like this makes the specific features of the tools more clear.
>  

Thanks for your comment; I was myself unsure about the wording. However,
this was meant to emphasize the nature of the tools in following the
UNIX style, but your suggestion is a bit wordy.

How about "UNIX-style phylogenetic analyses on trees and sequences"?

Thanks and regards
Afif

-- 
Afif Elghraoui | عفيف الغراوي
http://afif.ghraoui.name

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

[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++
  Description : phylogenetic analyses on trees and sequences for UNIX

 phyx provides a convenient, lightweight and inclusive toolkit consisting of
 programs spanning the wide breadth of programs utilized by researchers
 performing phylogenomic analyses. Modeled after Unix/GNU/Linux command
 line tools, individual programs perform a single task and operate on
 standard I/O streams. A result of this stream-centric approach is that, for
 most programs, only a single sequence or tree is in memory at any moment.
 Thus, large datasets can be processed with minimal memory requirements.
 phyx’s ever-growing complement of programs consists of over 35 programs
 focused on exploring, manipulating, analyzing and simulating phylogenetic
 objects (alignments, trees and MCMC logs). As with standard Unix command
 line tools, these programs can be piped (together with non-phyx tools),
 allowing the easy construction of efficient analytical pipelines.


This package will be maintained by the Debian Med team.

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

[Afif Elghraoui]

Hello,

There was a bioinformatics program I was considering packaging, but it
requires sbt to build and so I came across this ITP. I just have a
couple of comments on this bootstrapping situation.

On Sun, 05 Feb 2012 20:29:09 +0100 Mehdi Dogguy <me...@dogguy.org> wrote:
> On 05/02/12 18:35, Josh Suereth wrote:
> > As I stated before, I feel requiring SBT to build without itself is
> > like trying to build Debian without GCC.
> 
> Comparing this situation to "trying to build _gcc_ without _gcc_" would
> be a more fair comparison. (imho)
> 

I think it is actually more like trying to build `make` without `make`.
In fact, GNU make provides a shell script to build `make` if you don't
have an existing version to use [1], so it seems like a fair approach to
take here. I don't think the sbt developers should consider it offensive
to do so.

Bootstrapping a 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

[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 Lang: C++
  Description : data structures, algorithms, and utilities for C++ 
applications

pbcopper provides general tools for C++ applications. It is developed
for use by applications of the Pacific Biosciences SMRT Analysis
suite.

This package is a dependency of unanimity. It will be maintained by the Debian 
Med team.

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

[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 accurate genomic consensus sequences 
from single-molecule sequencing data

This package provides a common source for the related consensus processing
modules pbccs (for circular consensus sequencing), and the algorithms library
consensuscore2.

The consensuscore2 source package would be superceded by this one. pbccs hasn't
been packaged for Debian before, but would be newly provided by this unanimity
package.

Rudimentary packaging has been posted in the Debian Med team at
.
Anyone interested in helping with this should contact the Debian Med team 
.

Thanks and regards
Afif

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

[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 : alignment-based scrubbing pipeline for DNA sequencing reads

The Dazzler Scrubbing Suite produces a set of edited reads that are guaranteed
to
 * be continuous stretches of the underlying genome (i.e. no unremoved
   adapters and not chimers)
 * have no very low quality stretches (i.e. the error rate never exceeds some
   reasonable maximum, 20% or so in the case of Pacbio data).
Its secondary goal is to do so with the minimum removal of data and splitting
of reads.


This package will be maintained by Debian Med.

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

[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
  Description : small Pacific Biosciences datasets for testing

Utility and Python API for accessing representative Pacific Bioscience
sequencing data files for testing.

This package contains common test data files that will start being
used by the packages of the smrtanalysis suite for their test suites.
It will be maintained by Debian Med.

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

[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
  Description : generate consensus sequences for PacBio sequencing data

ConsensusCore2 embodies core C++ routines underlying the Arrow HMM
algorithm for PacBio multi-sequence consensus.  Arrow is the successor
to the Quiver model---a CRF model that was embodied in the
ConsensusCore C++ library. Compared to Quiver, the Arrow model is more
statistically principled and easier and more robust to train.


This package will become a Depends or Recommends of the pbgenomicconsensus
package. It will be maintained by the Debian Med team.

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

[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 الغراوي
http://afif.ghraoui.name

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

[Afif Elghraoui]

Package: wnpp
Severity: wishlist
Owner: Afif Elghraoui <a...@debian.org>

* Package name: sniffles
  Version : 0.0.1
  Upstream Author : Fritz Sedlazeck <fritz.sedlaz...@gmail.com>
* URL : https://github.com/fritzsedlazeck/Sniffles
* License : MIT
  Programming Lang: C++
  Description : structural variation caller using third-generation 
sequencing

 Sniffles is a structural variation caller using third-generation sequencing
 platforms such as those from Pacific Biosciences or Oxford Nanopore.
 It detects all types of SVs using evidence from split-read alignments,
 high-mismatch regions, and coverage analysis.


Packaging will be maintained by the Debian Med team.

Bug#811411: Maintainer upload is pending

[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

[Afif Elghraoui]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Hi, Marc,
I sent a request to join the alioth team for Adduser and you seem to
be the only project admin still active in Debian. I'm interested in
possibly adopting the package, so I've already converted the packaging
VCS to git and would like to publish that as part of the same project.

Many thanks and regards
Afif

- -- 
Afif Elghraoui | عفيف الغراوي
http://afif.ghraoui.name
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Bug#822661: ITP: python-et-xmlfile -- low memory Python library for creating large XML files

[Afif Elghraoui]

Package: wnpp
Severity: wishlist
Owner: Afif Elghraoui <a...@debian.org>
Control: block 822414 by -1

* Package name: python-et-xmlfile
  Version : 1.0.1
  Upstream Author : Charlie Clark <charlie.cl...@clark-consulting.eu> and Elias 
Rabel
* URL : https://bitbucket.org/openpyxl/et_xmlfile
* License : MIT
  Programming Lang: Python
  Description : low memory Python library for creating large XML files

et_xmlfile is a low memory library for creating large XML files.

It is based upon the xmlfile module from lxml with the aim of allowing
code to be developed that will work with both libraries.
It was developed initially for the openpyxl project but is now a standalone
module.


This package is a new dependency of openpyxl, but was swept under the rug in 
the Debian package, resulting in #822414.
It will be maintained in collab-maint.

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

[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
  Description : single-pass sequencing read accuracy improver

 Sprai is a tool to correct sequencing errors in single-pass reads for
 de novo assembly. It is originally designed for correcting sequencing
 errors in single-molecule DNA sequencing reads, especially in Continuous
 Long Reads (CLRs) generated by PacBio RS sequencers. The goal of Sprai is
 not maximizing the accuracy of error-corrected reads. Instead, Sprai aims
 at maximizing the continuity (i.e., N50 contig length) of assembled contigs
 after error correction.

This package will be maintained by the Debian Med team.

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

[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
  Description : circularize genome assemblies

Circlator is a tool to automate assembly circularization for bacterial and
small eukaryotic genomes and produce accurate linear representations of
circular sequences.

This package will be maintained by the Debian Med team.

Bug#807802: pbsuite to move ahead without fringe dependency

[Afif Elghraoui]

Control: unblock -1 by 807803

The new, experimental ComplexResolver feature of PBHoney is being
disabled in the Debian package until the Python intervaltree dependency
can be fulfilled in Debian. The reason for that package's absence in
Debian is described on the relevant ITP:
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

[Afif Elghraoui]

Hi,
Have you already contacted the Debichem team about this ITP for inchi?
Their mailing list is at <debichem-de...@lists.alioth.debian.org>.
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

[Afif Elghraoui]

Hello,
I've just about finalized the qsopt-ex package. This is an exact linear
programming solver that can be used by cobrapy (python-cobra) for
constraint-based systems biology models.

Could someone please upload to unstable?

git+ssh://git.debian.org/git/debian-med/qsopt-ex.git
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

[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.
>>>
>>
>> This is the package that you rejected last November because of the
>> non-free file dbmalloc.h [1]. The package has the +dfsg suffix because I
>> excluded the postscript Manual.ps which cannot be built from source.
>> It's my understanding that even non-free packages should meet the dfsg
>> as far as possible.
> 
> Sounds sensible.
>  
>> Would you prefer I put the Manual.ps back in so that there is no
>> repacked tarball? Otherwise, do you have a more appropriate alternative
>> to +dfsg for the repack suffix?
> 
> I do not think that the tarball name in itself should be a rejection
> reason.  I also use this suffix for repackaged tarballs.  Some people
> are using +ds but I'd consider this nitpicking.
>

According to uscan(1) [1], it does look like ds is more appropriate in
this case.


> BTW, did you possibly contact the copyright holders for choosing a
> free license?
>

I haven't. I'd have to do some investigative work to find a valid email
address, but I might as well do that now.

Thanks and regards
Afif

1. "Common suffixes might be +dfsg1 to indicate the removal of files
that are not DFSG-compliant or +ds1 for other reasons such as removal of
prebuilt files or large embedded code copies."

-- 
Afif Elghraoui | عفيف الغراوي
http://afif.ghraoui.name

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

[Afif Elghraoui]

Hello,

على الأربعاء  3 شباط 2016 ‫10:00، كتب Thorsten Alteholz:
> 
> as the authors do not mention the GPL version, it should be GPL-1+.
> 

This is now fixed in git. Could someone upload the corrected package?

git+ssh://git.debian.org/git/debian-med/poretools.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

[Afif Elghraoui]

Hi, Thorsten,

على الثلاثاء  2 شباط 2016 ‫04:00، كتب Thorsten Alteholz:
> 
> there seems to be something wrong with this package.
> A DFSG package should not be in non-free.
> 

This is the package that you rejected last November because of the
non-free file dbmalloc.h [1]. The package has the +dfsg suffix because I
excluded the postscript Manual.ps which cannot be built from source.
It's my understanding that even non-free packages should meet the dfsg
as far as possible.

Would you prefer I put the Manual.ps back in so that there is no
repacked tarball? Otherwise, do 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

[Afif Elghraoui]

Hi, Steffen,

على الإثنين 25 كانون الثاني 2016 ‫07:27، كتب Steffen Möller:
> Hi, I happily help with sponsoring 

That is much appreciated, but this package (together with nanopolish)
was already accepted :)

> and any feedback on how nice the
> nanopore is working for you would be appreciated :)

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

[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
* License : GPL
  Programming Lang: C
  Description : exact linear and integer programming solver

QSopt-ex is an implementation of a simplex-based algorithm that returns exact
rational solutions, taking advantage of the speed of floating-point
calculations and attempting to minimize the operations performed in
rational arithmetic.

A fork of the original project is maintained at 
, which is what will be targeted for the 
Debian packaging.
This program can be used as a backend solver for python-cobra, a systems biology
modeling toolkit. The package will be maintained by the Debian Med team.

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

[Afif Elghraoui]

Hi, Daniel,
I was filing an intent to package qsopt-ex for Debian. It is just part
of Debian procedure for introducing new packages and the fact that every
Debian ticket is called a bug is a bit unfortunate. I suppose you could
consider it a bug in Debian that qsopt-ex is not yet part of it, 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 Daniel Espinoza:
> Dear Afif,
> 
> I'm sorry, but I do not understand your e-mail. If I understand
> correctly, you are planning, or are already supporting this package
> (which makes me very happy indeed), but the header of your e-mail is
> referencing a bug... and then I'm at a loss.
> 
> Is this an automated mail?
> Best regards,
> Daniel E.
> 

Bug#811458: RFS: nanopolish

[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 | عفيف الغراوي
http://afif.ghraoui.name

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

[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++
  Description : library for reading Oxford Nanopore Fast5 files

Fast5 is a lightweight C++11 library to read raw signal data from Oxford
Nanopore's FAST5 files.

This package will be maintained by the Debian Med team. It is a requirement
for nanopolish.

Bug#811460: RFS: fast5

[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://afif.ghraoui.name

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

[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 for nanopore sequencing data

Nanopolish uses a signal-level hidden Markov model for consensus
calling of nanopore genome sequencing data.

This package will be maintained within the Debian Med team.

Bug#811154: RFS: poretools

[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 | عفيف الغراوي
http://afif.ghraoui.name

Bug#395843: wgs-assembler is now canu

[Afif Elghraoui]

Control: retitle -1 "ITP: canu -- single-molecule sequence assembler"

The Celera assembler website [1] now has a title that reads "If you are
assembling PacBio or Oxford Nanopore data, please use Canu [2] instead.
Celera Assembler is no longer being maintained."

Description:
Canu is a fork of the Celera Assembler designed for high-noise
single-molecule sequencing (such as the PacBio RSII or Oxford Nanopore
MinION). The software is currently alpha level, feel free to use and
report issues encountered.


1. http://wgs-assembler.sourceforge.net
2. http://canu.readthedocs.org/en/latest/
-- 
Afif Elghraoui | عفيف الغراوي
http://afif.ghraoui.name

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

[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 : toolkit for nanopore nucleotide sequencing data

poretools is a flexible toolkit for exploring datasets generated by
nanopore sequencing devices from MinION for the purposes of quality
control and downstream analysis. Poretools operates directly on the
native FAST5 (a variant of the HDF5 standard) file format produced by
ONT and provides a wealth of format conversion utilities and data
exploration and visualization tools.

This package will be maintained by the Debian Med team.
git://anonscm.debian.org/debian-med/poretools.git
http://anonscm.debian.org/cgit/debian-med/poretools.git

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

[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 : GPL
>   Programming Lang: C
>   Description : Efficiently extract arbitrary lines from a file or stream
> 
> Hail gets its name from a contraction of head and tail, the common alternative
> to this program. It extracts lines from a file, taken on stdin, and prints 
> them
> on stdout. It's so simple that the Unix wizards of old never bothered.
> 

You might like to try getting this program into moreutils [1].


> Hail will be co-maintained in the Debian Med team.
> 

1. https://joeyh.name/code/moreutils/

regards
Afif

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

[Afif Elghraoui]

Hello,

على الأربعاء 23 كانون الأول 2015 ‫03:59، كتب Wouter Verhelst:
>> Sorry for slacking - I tried to keep up with the spam on pkg-gridengine,
>> > but I've no real excuse for answering your earlier mail apart from
>> > generally being behind on Debian stuff.
>> > 
>> > I've made you and Dave admins on the Alioth project now, but if you
>> > prefer to maintain gridengine in another way, that's fine with me, too.
>> >

Many thanks-- I'll take it off collab-maint and start using the alioth
project, now that I can 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 kindly offered to sponsor as he said above.


Many thanks and regards
Afif

-- 
Afif Elghraoui | عفيف الغراوي
http://afif.ghraoui.name

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

[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 : sensitive variant calling from sequencing data

 LoFreq* (i.e. LoFreq version 2) is a fast and sensitive
 variant-caller for inferring SNVs and indels from next-generation
 sequencing data. It makes full use of base-call qualities and other
 sources of errors inherent in sequencing (e.g. mapping or base/indel
 alignment uncertainty), which are usually ignored by other methods or
 only used for filtering.
 .
 LoFreq* can run on almost any type of aligned sequencing data
 (e.g. Illumina, IonTorrent or Pacbio) since no machine- or
 sequencing-technology dependent thresholds are used. It automatically
 adapts to changes in coverage and sequencing quality and can
 therefore be applied to a variety of data-sets e.g.
 viral/quasispecies, bacterial, metagenomics or somatic data.
 .
 LoFreq* is very sensitive; most notably, it is able to predict
 variants below the average base-call quality (i.e. sequencing error
 rate). Each variant call is assigned a p-value which allows for
 rigorous false positive control. Even though it uses no
 approximations or heuristics, it is very efficient due to several
 runtime optimizations and also provides a (pseudo-)parallel
 implementation. LoFreq* is generic and fast enough to be applied to
 high-coverage data and large genomes. On a single processor it takes
 a minute to analyze Dengue genome sequencing data with nearly 4000X
 coverage, roughly one hour to call SNVs on a 600X coverage E.coli
 genome and also roughly an hour to run on a 100X coverage human exome
 dataset.



This package will be maintained by the Debian Med team.

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

[Afif Elghraoui]

Hi,
As I've made numerous requests on this list [1-3] and tried twice to
directly contact Michael Banck, one of the two Alioth team admins
(both of them CC'd here this time), regarding membership on the team
so that I could work on updating the gridengine package using the
team's repository.

I have so far been working from my personal fork at
<http://anonscm.debian.org/cgit/users/afif-guest/gridengine.git/>, but
I'm now going to be using collab-maint as I said previously [4].

I have created the repository on collab-maint:
http://anonscm.debian.org/cgit/collab-maint/gridengine.git/

This is what I'll be using from now on.

regards
Afif

1.
https://lists.alioth.debian.org/pipermail/pkg-gridengine-devel/2015-August/000759.html
2.
https://lists.alioth.debian.org/pipermail/pkg-gridengine-devel/2015-September/000763.html
3.
http://lists.alioth.debian.org/pipermail/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: ITP: falconkit -- genome assembly toolkit

[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
  Description : genome assembly toolkit

Falcon is a set of tools for fast aligning long reads for consensus and
assembly. It is a simple code collection for efficient assembly of haploid and
diploid genomes.


This package is needed for parts of wgs-assembler and will be handled by
the Debian Med team.

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

[Afif Elghraoui]

Hi, all,
I ended up packaging falconkit 0.1.3, as that's what's required for
wgs-assembler. Although there are newer releases, they are not
compatible and the software is not really mature enough in any case.

I believe this is the last blocker for wgs-assember. The packaging is 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#807804: status of packaging intervaltree

[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

[Afif Elghraoui]

Hi, all,
I've completed preparation of the pbbarcode package. Could someone
please sponsor this? The git repository is at

git+ssh://git.debian.org/git/debian-med/pbbarcode.git

and browsable at
http://anonscm.debian.org/cgit/debian-med/pbbarcode.git


I've tagged the commit--- if the 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

[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 Lang: Python
  Description : annotate PacBio sequencing reads with barcode information

The pbbarcode package provides tools for annotating PacBio sequencing reads
with barcode information. Typically, pbbarcode is called in context of a
SMRTPipe workflow as opposed to directly on the command line, however, users
are encouraged to utilize the command-line utility directly, as more options
are available.
.
This package is part of the SMRTAnalysis suite.

This package will be maintained by the Debian Med team.

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

[Afif Elghraoui]

Package: wnpp
Severity: wishlist
Owner: Afif Elghraoui <a...@ghraoui.name>
Control: block 807803 by -1

* Package name: python-intervaltree
  Version : 2.1.0
  Upstream Author : Chaim-Leib Halbert <chaim.leib.halb...@gmail.com>
* URL : https://github.com/chaimleib/intervaltree
* License : Apache 2.0
  Programming Lang: Python
  Description : mutable, self-balancing interval tree

A mutable, self-balancing interval tree for Python 2 and 3
where queries may be by point, by range overlap, or by range
envelopment. This library was designed to allow tagging text
and time intervals, where the intervals include the lower bound
but not the upper bound.

I'm planning to maintain the package within the python modules
team after I read up on using the git-dpm packaging system.

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

[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
  Description : software for Pacific Biosciences sequencing data

The PBSuite contains two projects created for analysis of
Pacific Biosciences long-read sequencing data.
* PBJelly - genome upgrading tool
* PBHoney - structural variation discovery

This package will be managed by the Debian Med team.

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

[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
  Programming Lang: Python
  Description : Interval tree convenience classes for genomic data

Convenience classes for loading UCSC genomic annotation records into
a set of interval tree data structures.

This package is needed by the pbhoney package of the pbsuite
and will be built and maintained by the Debian Med team.

Bug#796644: RFS: pbdagcon (unstable NEW)

[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 | عفيف الغراوي
http://afif.ghraoui.name

Bug#797676: RFS: kineticstools (unstable NEW)

[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
http://afif.ghraoui.name

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

[Afif Elghraoui]

Hi, ftp-masters,
I was wondering if it's possible to have some expedited processing for
this package, pbseqlib. The sources for this are already included in the
current blasr package, but I packaged it separately here since it turns
out this specialized library is used by one other package (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 package has been uploaded:
> 
>  رسالة ممرّرة 
> الموضوع: pbseqlib_0~20151014+gitbe5d1bf-1_amd64.changes is NEW
> التاريخ: Tue, 17 Nov 2015 07:48:58 +
> مِن: Debian FTP Masters <ftpmas...@ftp-master.debian.org>
> إلى: Debian Med Packaging Team
> <debian-med-packag...@lists.alioth.debian.org>, Afif Elghraoui
> <a...@ghraoui.name>, ti...@debian.org
> 
> binary:libblasr is NEW.
> binary:libblasr-dev is NEW.
> binary:libpbdata is NEW.
> binary:libpbdata-dev is NEW.
> binary:libpbihdf is NEW.
> binary:libpbihdf-dev is NEW.
> binary:libpbseq is NEW.
> binary:libpbseq-dev is NEW.
> source:pbseqlib is NEW.
> 
> Your package has been put into the NEW queue, which requires manual action
> from the ftpteam to process. The upload was otherwise valid (it had a good
> OpenPGP signature and file hashes are valid), so please be patient.
> 
> Packages are routinely processed through to the archive, and do feel
> free to browse the NEW queue[1].
> 
> If there is an issue with the upload, you will receive an email from a
> member of the ftpteam.
> 
> If you have any questions, you may reply to this email.
> 
> [1]: https://ftp-master.debian.org/new.html
> 
> 
> 

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

[Afif Elghraoui]

Hi, Andreas,
I looked to see if there was some way to get around this problem. I
found an apparently free implementation of the dbmalloc interface as
part of mpatrol [1], but mpatrol is no longer in Debian [2] and it's
probably not sensible to try to reintroduce it.

I might also suggest to upstream to consider alternative projects that
provide similar functionality [3], but development of this software is
not particularly active (though I think the package itself is still
useful), so I do not think upstream will be handling this issue soon.

I will still contact them to see if they want 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 Elghraoui | عفيف الغراوي
http://afif.ghraoui.name

On الخميس 26 تشرين الثاني 2015 14:01, Thorsten Alteholz wrote:
> 
> Hi Afif,
> 
> after a short glimpse, I have to reject your package as I am not allowed to 
> modify dbmalloc.h
> 
>   Thorsten
> 
> ===
> 
> Please feel free to respond to this email if you don't understand why
> your files were rejected, or if you upload new files which address our
> concerns.
> 
> 

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

[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 add the missing MIT license of python-pbcommand-0.2.16/tests/* 
> to your debian/copyright.
> 
> Thanks!
>  Thorsten
> 
> ===
> 
> Please feel free to respond to this email if you don't understand why
> your files were rejected, or if you upload new files which address our
> concerns.
> 
> 

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

[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 : Apache
  Programming Lang: Perl
  Description : Ensembl tools for genomic data processing

Ensembl (http://www.ensembl.org) is a genomic interpretation system providing
the most up-to-date annotations, querying tools and access methods for
chordates and key model organisms.
.
The tools include the Variant Effect Predictor, Assembly Converter,
ID History Converter, and Region Reporter utilities.


This package will be maintained by the Debian Med team.

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

[Afif Elghraoui]

Package: wnpp
Severity: wishlist
Owner: Afif Elghraoui <a...@ghraoui.name>

* Package name: pyconfigure
  Version : 0.2.2
  Upstream Author : Brandon Invergo <bran...@invergo.net>
* URL : https://www.gnu.org/software/pyconfigure/
* License : GPL
  Programming Lang: Python
  Description : automatic configure script builder for Python software

GNU pyconfigure provides developers with file templates for implementing
standard `configure' scripts and `Makefile' recipes for their Python packages.
pyconfigure supports different project needs, allowing you to write your
build/install logic in Python or in Make. Developers with existing packages
need not worry, as pyconfigure integrates well with what you have already
written.
.
While the goal is to make it easier for Python packages to provide the
standard configuration and installation procedure, pyconfigure also offers
other advantages over the traditional Python-based methods. Because much of
pyconfigure is based upon the powerful GNU Autoconf, packages that use
additional languages such as C or Fortran automatically benefit from existing
support without having to hack it in oneself, as in other Python-based
solutions. Opting to use Make to write your installation logic provides you
with a powerful, robust and flexible system that has been designed
specifically with such processes in mind.


I am currently a DM and will be needing a sponsor for this package.
I intend to push the packaging repository to collab-maint once it's ready.

Bug#805607: RFS: piler - genomic repeat discovery

[Afif Elghraoui]

Hi, team,
I just packaged piler. Could someone please upload to unstable?

git+ssh://git.debian.org/git/debian-med/piler.git
http://anonscm.debian.org/cgit/debian-med/piler.git

Although the cgit link may need a few minutes since I just created the
repository.

Many thanks and regards
Afif

-- 
Afif Elghraoui | عفيف الغراوي
http://afif.ghraoui.name

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

[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 repeat analysis

PILER (Parsimonious Inference of a Library of Elementary Repeats)
searches a genome sequence for repetitive elements. It implements search
algorithms that identify characteristic patterns of local alignments
induced by certain classes of repeats.

This package will be maintained by the Debian Med team.

Bug#798218: RFS: pbseqlib (unstable)

[Afif Elghraoui]

Hi, team,
I finally got around to finishing up the pbseqlib package. I first
thought these libraries were only used by blasr, so the blasr package
currently includes their sources and statically links to them.

It however turns out to also be used by pbdagcon (#796644), so I thought
I'd package it separately for both packages to share.
pbdagcon in turn is needed for parts of wgs-assembler (#395843), so I
set the urgency of this upload to 'medium'.

The repository for pbseqlib is at:

git+ssh://git.debian.org/git/debian-med/pbseqlib.git
http://anonscm.debian.org/cgit/debian-med/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: ITP: python-pymummer -- Python interface to MUMmer

[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: Python
  Description : Python interface to MUMmer

pymummer is a Python wrapper for running the program of the MUMmer
sequence alignment suite and parsing its output.

This package will be maintained by the Debian Med team.

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

[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
http://afif.ghraoui.name

Bug#804007: RFS: bcftools

[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: ITP: bcftools -- utilities for genomic variant calling and manipulating VCF and BCF files

[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
  Description : utilities for genomic variant calling and manipulating VCF 
and BCF files

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

Most commands accept VCF, bgzipped VCF and BCF with filetype detected
automatically even when streaming from a pipe. Indexed VCF and BCF will work
in all situations. Un-indexed VCF and BCF and streams will work in most,
but not all situations.

BCFtools is designed to work on a stream. It regards an input file "-" as the
standard input (stdin) and outputs to the standard output (stdout). Several
commands can thus be combined with Unix pipes.


This package will be managed by the Debian Med team.

Bug#804007: pre-existing git repository for bcftools

[Afif Elghraoui]

Hi, team,
Before filing the ITP just now, I wanted to make sure I could get the
package to build. After I achieved that, I went to create the git
repository on Alioth but found out there was an old attempt for
packaging it there.

As I've already made good progress on the package starting 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#803542: RFS: trnascan-se (NEW)

[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
http://afif.ghraoui.name

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

[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 : detection of transfer RNA genes in genomic sequence

tRNAscan-SE identifies 99-100% of transfer RNA genes in DNA sequence while
giving less than one false positive per 15 gigabases. Two previously described
tRNA detection programs are used as fast, first-pass prefilters to identify
candidate tRNAs, which are then analyzed by a highly selective tRNA covariance
model. This work represents a practical application of RNA covariance models,
which are general, probabilistic secondary structure profiles based on
stochastic context-free grammars. tRNAscan-SE searches at ~ 30 000 bp/s.
Additional extensions to tRNAscan-SE detect unusual tRNA homologues such as
selenocysteine tRNAs, tRNA-derived repetitive elements and tRNA pseudogenes.

This package is useful for genome annotations and will be managed by the
Debian Med team.

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

[Afif Elghraoui]

Hello,

On الثلاثاء 27 تشرين الأول 2015 09:00, Thorsten Alteholz wrote:
> 
> Hi Afif,
> 
> please mention all files that are licensed under LGPL in your 
> debian/copyright.
> 

I'm sorry about that-- I could've sworn I had it right. I think it
should be good now. Andreas, 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)

[Afif Elghraoui]

Hi, all,
I've finished preparing the python-pbcommand package. This is part of
the smrtanalysis suite for long-read DNA sequencing data analysis.

git+ssh://git.debian.org/git/debian-med/python-pbcommand.git
http://anonscm.debian.org/cgit/debian-med/python-pbcommand.git

Many thanks and regards
Afif

-- 
Afif Elghraoui | عفيف الغراوي
http://afif.ghraoui.name

Bug#802041: RFS: python-avro

[Afif Elghraoui]

Hi, team,
I have finished preparing the python-avro package. I need this one
because it's a dependency of python-pbcommand, which is part of the
dependency chain in smrtanalysis.

git+ssh://git.debian.org/git/debian-med/python-avro.git
http://anonscm.debian.org/cgit/debian-med/python-avro.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

[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
  Description : genome browser and annotation tool

Artemis is a genome browser and annotation tool that allows visualisation of
sequence features, next generation data and the results of analyses within the
context of the sequence, and also its six-frame translation.

This is one of the packages on the "Debian Med's Most Wanted" list.

There is already an ITP for this package from over 15 years ago [1],
apparently predating wnpp bug reports. This package will be handled by
the Debian Med team.

1. https://lists.debian.org/debian-devel/1999/07/msg00020.html

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

[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: Python
  Description : Python API to the Apache Avro data serialization system

Avro is a data serialization system that provides
- Rich data structures.
- A compact, fast, binary data format.
- A container file, to store persistent data.
- Remote procedure call (RPC).


This package is a dependency of python-pbcommand (#798872). It will be
maintained by the Debian Med team.

Bug#794447: RFS: pbgenomicconsensus (NEW)

[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://afif.ghraoui.name



signature.asc
Description: OpenPGP digital signature

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

[Afif Elghraoui]

Hi, all,

I've done most of my work in Debian Med, not so much in Debian Science.
This package (CyLP) is a Python interface to COIN-OR. I packaged
python-cobra (aka cobrapy), which can use this as a solver interface and
Debian packaging for CyLP was requested by the cobrapy developer. I'm
not actually very concerned with it, so I filed an RFP on his behalf [1].

The RFP apparently didn't go anywhere where anyone would see it, so I
thought I would get the packaging started myself. Again, I am not really
interested in maintaining it myself, so I'm hoping to renew the RFP and
provide the groundwork for the package if anyone here can take over it.

The initial packaging is now in Debian Science git:
http://anonscm.debian.org/cgit/debian-science/packages/python-cylp


Some notes for anyone interested in taking up this package:
* Some of the source files (see d/copyright for the exact file names)
are copyright IBM with a header that only says "All Rights Reserved", so
that will require some clarification from upstream.

* The package currently does not build: upstream provides pre-cythonized
files. Using these, the C/CXX codes compile, but one of the tests failed
with a segmentation fault error. I overrode the d/rules clean target to
get rid of the cythonized files so that they are freshly generated with
each build, but there is then one file that fails to cythonize.

* I have a branch set up where Python3 packaging can be attempted (named
topic/python3-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

[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 library for the dazzler assembler

 To facilitate the multiple phases of the dazzler assembler, all the read
 data are organized into what is effectively a "database" of the reads and
 their meta-information. The design goals for this database are as follows:
 (1) The database stores the source Pacbio read information in such a way that
 it can recreate the original input data, thus permitting a user to remove
 the (effectively redundant) source files. This avoids duplicating the
 same data, once in the source file and once in the database.
 (2) The database can be built up incrementally, that is new sequence data can
 be added to the database over time.
 (3) The database flexibly allows one to store any meta-data desired for reads.
 This is accomplished with the concept of *tracks* that implementors can
 add as they need them.
 (4) The data is held in a compressed form equivalent to the .dexta and .dexqv
 files of the data extraction module. Both the .fasta and .quiva
 information for each read is held in the database and can be recreated
 from it. The .quiva information can be added separately and later on if
 desired.
 (5) To facilitate job parallel, cluster operation of the phases of dazzler,
 the data base has a concept of a *current partitioning* in which all the
 reads that are over a given length and optionally unique to a well, are
 divided up into *blocks* containing roughly a given number of bases,
 except possibly the last block which may have a short count. Often
 programs con be run on blocks or pairs of blocks and each such job is
 reasonably well balanced as the blocks are all the same size. One must
 be careful about changing the partition during an assembly as doing so can
 void the structural validity of any interim block-based results.

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

[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 Lang: Python
  Description : common command-line interface for Pacific Biosciences 
analysis modules

To integrate with the pbsmrtpipe workflow engine, you must to be able to
generate a Tool Contract and to be able to run from a Resolved Tool Contract.
A Tool Contract contains the metadata of the exe, such as the file types of
inputs, outputs and options.
There are two principal use cases, first wrapping/calling python functions that
have been defined in external python packages, or scripts. Second, creating a
CLI tool that supports emitting tool contracts, running resolved tool contracts
and complete argparse-style CLI.


This package is part of the SMRT Analysis suite and is to be handled by
the Debian Med team.

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

[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, Afif Elghraoui wrote:
>>
>>> The binary package is still called python-pbalign
>>> because it does include public python modules..
>>
>> Does not sound logical.  Assume there might be some python3-pbalign
>> sooner or later.  Then you want to provide both python-pbalign and
>> python3-pbalign.  Where do you want to put the scripts then?  So if you
>> ask me spliting the commandline tools to a separate package pbalign
>> would be the best solution even now.
>>  
> 
> I thought about this, but the reason I didn't do it is that the scripts
> are basically just wrappers around the library. A python3 version would
> then have its own version of the scripts.
> 
> I suppose this could be made to work by making the pbalign package
> depend on python-pbalign, which would contain the libraries, while then
> ignoring any of the scripts from a python3 version of the package. I
> like this way better because the use case of the package as a library is
> a very uncommon one-- and the API is not really documented, either. All
> documentation is for the command-line use case.
> 
> So I'll try this and report back.
> 

-- 
Afif Elghraoui | عفيف الغراوي
http://afif.ghraoui.name

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

[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
  Programming Lang: C++
  Description : libraries for analyzing Pacific Biosciences sequences

 These are libraries used by blasr and other executables such as samtoh5,
 loadPulses for analyzing Pacific Biosciences sequences.This library contains
 three sub-libraries, including pbdata, hdf and alignment:
 * libpbdata:
  library for handling Pacbio sequencing data
 * libpbhdf:
  library for handling Pacbio hdf5 files (e.g., *.pls.h5, *.rgn.h5, *.bas.h5)
 * libblasr:
  library for aligning Pacbio reads to target sequences used in blasr


This package is part of the SMRT Analysis suite. It will be maintained by the
Debian Med team.

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

[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 : Pacific Biosciences binary alignment/map (BAM) library

 The BAM format is a binary, compressed, record-oriented container format
 for raw or aligned sequence reads. The associated SAM format is a text
 representation of the same data. The specifications for BAM/SAM are maintained
 by the SAM/BAM Format Specification Working Group.
 .
 PacBio-produced BAM files are fully compatible with the BAM specification,
 but makes use of the extensibility mechanisms of the BAM specification to
 encode PacBio-specific information. The pbbam library provides tools to
 work with these files

Bug#797675: RFS: pbalign (NEW)

[Afif Elghraoui]

Hi, all,
I've completed the pbalign package--- I renamed the source package from
python-pbalign to just pbalign since it is primarily used as a set of
command line tools. The binary package is still called python-pbalign
because it does include public python modules..

The repository on Alioth 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)

[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

[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 testing framework for command line applications

Cram is a functional testing framework for command line applications based on
Mercurial's unified test format. Cram runs each command and compares the
command output in the test with the command's actual output.


At least two packages (marked as affected by this RFP) have test suites that
rely on this program and currently cannot be run on autopkgtest because of
cram's absence in Debian.

The repository with most recent activity appears to be the one on github
(linked above), but there is also a copy on bitbucket:
https://bitbucket.org/brodie/cram/src

and this is the pypi page:
https://pypi.python.org/pypi/cram

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

[Afif Elghraoui]

Hi, Andreas,

On الثلاثاء  1 أيلول 2015 03:06, Andreas Tille wrote:
> I noticed that there is no information about pbdagcon in Debian Med git
> which could be fetched by the metadata gatherer to make it available on
> the tasks pages.  In case you have some local Git it would help if you
> could push the current state.
> 

There is not yet any local git either. I am filing ITPs (since there
apparently can't be a team-owned RFP) for all the components of
smrtanalysis. I'll then tackle them all, but this way, it's more clear
to everyone and me what needs to be done 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

[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
  Programming Lang: Python
  Description : detecting DNA modifications from single molecule, real-time 
sequencing data

kineticsTool loads IPDs observed at each position in the genome, and compares
those IPDs to value expected for unmodified DNA, and outputs the result of
this statistical test. The expected IPD value for unmodified DNA can come
from either an in-silico control or an amplified control. The in silico control
is trained by PacBio and shipped with the package. It predicts predicts the
IPD using the local sequence context around the current position. An amplified
control dataset is generated by sequencing unmodified DNA with the same
sequence as the test sample. An amplified control sample is usually generated
by whole-genome amplification of the original sample.

This package is part of the SMRT Analysis suite and is to be handled by the
Debian Med team.

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

[Afif Elghraoui]

Package: wnpp
Severity: wishlist
Owner: Debian Med Packaging Team debian-med-packag...@lists.alioth.debian.org

* Package name: daligner
  Version : 1.0
  Upstream Author : Eugene W. Myers, Jr. gene.my...@gmail.com
* URL : http://github.com/thegenemyers/DALIGNER
* License : BSD
  Programming Lang: C
  Description : local alignment discovery between long nucleotide 
sequencing reads

These tools permit one to find all significant local alignments between
reads encoded in a Dazzler database. The assumption is that the reads are
from a Pacific Biosciences RS II long read sequencer. That is, the reads
are long and noisy, up to 15% on average.

This package is being prepared by the Debian Med team.
git://anonscm.debian.org/debian-med/daligner.git
http://anonscm.debian.org/cgit/debian-med/daligner.git

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

[Afif Elghraoui]

Hi, Andreas,

On الخميس 27 آب 2015 23:50, Andreas Tille wrote:
 Hi Afif,
 
 I stumbled upon the quite short description which is not very clear for
 outsiders.  I think this publication
 
http://www.ncbi.nlm.nih.gov/pubmed/26006009
 
 might be related.  If so please add a debian/upstream/metadata file to
 mention this and add some parts of the abstract to the long description.


At the time I did the initial packaging, I wasn't aware of the paper and
took the descriptions from the upstream github page. This should be no
problem, but I won'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

[Afif Elghraoui]

Package: wnpp
Severity: wishlist
Owner: Debian Med Packaging Team debian-med-packag...@lists.alioth.debian.org
Control: block 787977 by -1

* Package name: pbdagcon
  Version : git1d12e13
  Upstream Author : Pacific Biosciences dev...@pacificbiosciences.com
* URL : https://github.com/PacificBiosciences/pbdagcon
* License : BSD**
  Programming Lang: C++, Python
  Description : sequence consensus algorithm implementation based on 
directed acyclic graphs

pbdagcon is a tool that implements DAGCon (Directed Acyclic Graph Consensus),
which is a sequence consensus algorithm based on using directed acyclic graphs
to encode multiple sequence alignment.
.
It uses the alignment information from blasr to align sequence reads to a
backbone sequence. Based on the underlying alignment directed acyclic graph,
it will be able to use the new information from the reads to find the
discrepancies between the reads and the backbone sequences. A dynamic
programming process is then applied to the DAG to find the optimum sequence of
bases as the consensus. The new consensus can be used as a new backbone
sequence to iteratively improve the consensus quality.

This package is part of the SMRTAnalysis suite and also a dependency of
wgs-assembler. It will be handled by the Debian Med team.

** I'm double-checking the license of this component at 
https://github.com/PacificBiosciences/pbdagcon/issues/40.

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

[Afif Elghraoui]

Package: wnpp
Severity: wishlist
Owner: Debian Med Packaging Team debian-med-packag...@lists.alioth.debian.org
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
  Description : Random number generators, probability distributions, 
combinatorics and statistics for Java

The Uncommons Maths library provides five easy-to-use, statistically sound,
high-performance pseudorandom number generators (RNGs). They are:
 * MersenneTwisterRNG
A Java port of the fast and reliable Mersenne Twister RNG originally
developed by Makoto Matsumoto and Takuji Nishimura.
 * XORShiftRNG
A Java implementation of the very fast PRNG described by George Marsaglia.
It has a period of about 2160, which although much shorter than the
Mersenne Twister's, it can be up to twice as fast.
 * CMWC4096RNG
A Java implementation of a Complementary-Multiply-With-Carry (CMWC) RNG as
described by George Marsaglia. It has an extremely long period (2131104)
and performance comparable to the Mersenne Twister (though the Mersenne
Twister has the advantage of only requiring 16 bytes of seed data rather
than the 16 kilobytes required by the CMWC RNG). 
 * AESCounterRNG
This is a cryptographically-strong1 non-linear RNG that is around 10x
faster than java.security.SecureRandom. Reverse-engineering the generator
state from observations of its output would involve cracking the AES block
cipher. 
 * CellularAutomatonRNG
A Java port of Tony Pasqualoni's fast Cellular Automaton RNG. It uses a
256-cell automaton to generate random values. 

This package is a dependency of wgs-assembler and will be handled by the
Debian Med team.

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

[Afif Elghraoui]

Package: wnpp
Severity: wishlist
Owner: Debian Med Packaging Team debian-med-packag...@lists.alioth.debian.org
Control: block 395843 by -1

* Package name: mhap
  Version : 1.6
  Upstream Author : Sergey Koren ser...@umd.edu, Konstantin Berlin 
kber...@umd.edu
* URL : https://github.com/marbl/MHAP
* License : Apache
  Programming Lang: Java
  Description : locality-sensitive hashing to detect long-read overlaps

MinHash alignment process (MHAP pronounced MAP): locality-sensitive hashing
to detect DNA sequencing long-read overlaps and utilities.


This package is a dependency of wgs-assembler and will be handled by the
Debian Med packaging team.

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

[Afif Elghraoui]

Package: wnpp
Severity: wishlist

* Package name: python-cylp
  Version : 0.7.2
  Upstream Author : Mehdi Towhidi mehdi.towh...@gerad.ca
* URL : https://github.com/coin-or/CyLP
* License : CPL
  Programming Lang: Python
  Description : Python interface to COIN-OR linear and mixed-integer 
program solvers

CyLP is a Python interface to COIN-OR’s Linear and mixed-integer program
solvers (CLP, CBC, and CGL). CyLP’s unique feature is that it can be used
to alter the solution process of the solvers from within Python. For example,
cut generators, branch-and-bound strategies, and primal/dual Simplex pivot
rules can be defined completely in Python.

I am filing this request on behalf of the python-cobra upstream developer.
If this request is fulfilled, python-cylp would be added as a Recommends for
python[3]-cobra.

Bug#787982: python-pbh5tools ready to upload

[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

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

[Afif Elghraoui]

Package: wnpp
Severity: wishlist
Owner: Debian Med Packaging Team debian-med-packag...@lists.alioth.debian.org
Control: block 794447 by -1

* Package name: pb-consensuscore
  Version : 1.0.0
  Upstream Author : Pacific Biosciences dev...@pacificbiosciences.com
* URL : https://github.com/PacificBiosciences/ConsensusCore
* License : BSD
  Programming Lang: C++, Python
  Description : library of multiple nucleotide sequence consensus routines

ConsensusCore is a library of algorithms for Pacific Biosciences multiple
sequence consensus that powers Quiver, a variant and consensus caller
for single-molecule sequencing reads.

This package is a dependency of pb-genomicconsensus (#794447), a component of
the SMRTAnalysis suite (#787977). These are to be built and maintained by the
Debian Med team.


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

[Afif Elghraoui]

Package: wnpp
Severity: wishlist
Owner: Debian Med Packaging Team debian-med-packag...@lists.alioth.debian.org
Control: block 787977 by !

* Package name: pb-genomicconsensus
  Version : 1.0.0
  Upstream Author : Pacific Biosciences dev...@pacificbiosciences.com
* URL : https://github.com/PacificBiosciences/GenomicConsensus
* License : BSD
  Programming Lang: Python
  Description : Pacific Biosciences variant and consensus caller

The GenomicConsensus package provides Quiver, Pacific Biosciences'
flagship consensus and variant caller. Quiver is an algorithm that finds
the maximum likelihood template sequence given PacBio reads of the template.
These reads are modeled using a conditional random field approach that
prescribes a probability to a read given a template sequence. In addition to
the base sequence of each read, Quiver uses several additional quality value
covariates that the base caller provides.

This package is part of the SMRTAnalysis suite (#787977), to be built and
maintained by the Debian Med team.


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

[Afif Elghraoui]

Hello,
I'm contacting you on behalf of the Debian Med team, a group within the
Debian project that packages software for biology and medicine. You can
find a list of our work on biology software projects at
http://blends.debian.org/med/tasks/bio

I've taken up the task of bringing in the SMRTAnalysis suite and its
dependencies as a set of official Debian packages. pbcore has already
been included into Debian [1]. pbh5tools is next in that dependency
chain [2]. I've also been working on bringing in Celera Assembler; its
own dependency kmer has been packaged and is awaiting processing by the
Debian ftpmasters [3].

Besides just notifying you of the effort, I'd like to note that it will
be difficult to include into Debian new Python packages that do not
support Python 3 [4-5]. For pbcore, I have made the transition myself[6]
with the intent to forward the patches. Since this will be an issue with
the other Python packages comprising SMRTAnalysis, I would like to see
if we can cooperate to support Python3. I can help with the first step
of the transition, but would you be willing to maintain compatibility
with both Python2 and Python3 versions?

Thank you very much for providing SMRTAnalysis as unrestricted software.
I am personally a regular user of this software.

Many thanks and regards

Afif


1. https://packages.qa.debian.org/p/python-pbcore.html
2. https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=787982
3. https://ftp-master.debian.org/new/kmer-tools_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



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

[Afif Elghraoui]

Package: wnpp
Severity: wishlist
Owner: Afif Elghraoui a...@ghraoui.name
X-Debbugs-Cc: debian-de...@lists.debian.org

* Package name: ori
  Version : 0.8.1
  Upstream Author : Stanford University orifs-de...@lists.stanford.edu
* URL : http://ori.scs.stanford.edu/
* License : ori (MIT-like)
  Programming Lang: C++
  Description : secure distributed file system

Ori is a distributed file system built for offline operation and empowers
the user with control over synchronization operations and conflict 
resolution.

History is provided through lightweight snapshots and users can verify that
the history has not been tampered with. Through the use of replication,
instances can be resilient and recover damaged data from other nodes.


I will need a sponsor for this package. I am currently packaging on
my local machine using git-build-package and may publish the repository
on my own git server or seek access on collab-maint.

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

[Afif Elghraoui]

On الجمعـة 17 تـمـوز 2015 21:15, Troy Benjegerdes wrote:
 This is very interesting, does Ori have an active developer and user
 community?



Not extemely active since it doesn't seem word has spread very far. The
last activity on the mailing list is from a month ago [1].


 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


Regards
Afif


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Bug#787981: Request for Sponsorship - python-pbcore

[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

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Bug#787981: Status of python-pbcore

[Afif Elghraoui]

This package does not yet have python3 support. That can be added, but 
the tests must be run to make sure the porting is successful. As 
python-pbcore has a run-time dependency on a version of python-pysam not 
yet in unstable, running the test suite using the official Debian 
packages is not yet possible.


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Bug#787982: pbh5tools status

[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.


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