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Re: Please do not hide clearly bioinformatics related stuff in language teams (Was: Bug#961730: ITP: presto -- REpertoire Sequencing TOolkit)

Hi Andreas,

Thank you for asking. I am fine with just about everything, really. It
is its reverse dependencies I am interested in who to the best to my
knowledge do not make use of any executable.



On 28.05.20 15:43, Andreas Tille wrote:
Hi Steffen,

well, its probably my fault to not have checked tasks for the string
presto but this name was pretty new to me and I admit I would not have
assumed that something which I consider rather a user application
toolset is prefixed by python3 in the package name.  I'd love that we in
the Debian Med team would agree that it makes no sense to move the
software we are packaging into "random" language teams without really
good reasons.

Currently we have bio-ruby inside the Ruby team since they have asked
for maintaining it (which makes sense since we have no Ruby competence
here).  We have golang-github-biogo-hts-dev in pkg-go team for similar
reasons.  There are also quite some Perl modules maintained by pkg-perl
team and I admit I'm not really happy about having some Perl modules
here and some there.  However, the Uploaders of these packages have at
least discussed this here.

For presto I definitely see no reason and I'd love to move the package
to Debian Med (surely after I have removed my duplicated work - but
I realised that I have at least not written the manpages vainly. ;-) )

I noticed that python3-presto is actually used in changeo as a module
while I was foxussing on the user application.  Once we are touching
the package do we want to split the binary into

    presto   and


I'd volunteer to move the package (which we should do IMHO in any
case) and if you agree also doing the split of the binary package.

Kind regards


On Thu, May 28, 2020 at 03:22:36PM +0200, Andreas Tille wrote:
Package: wnpp
Severity: wishlist

Subject: ITP: presto -- REpertoire Sequencing TOolkit
Package: wnpp
Owner: Andreas Tille <tille@debian.org>
Severity: wishlist

* Package name    : presto
   Version         : 0.6.0
   Upstream Author : Kleinstein Lab, Yale University
* URL             : https://presto.readthedocs.io/
* License         : AGPL-3
   Programming Lang: Python
   Description     : REpertoire Sequencing TOolkit
  pRESTO is a toolkit for processing raw reads from high-throughput
  sequencing of B cell and T cell repertoires.
  Dramatic improvements in high-throughput sequencing technologies now
  enable large-scale characterization of lymphocyte repertoires, defined
  as the collection of trans-membrane antigen-receptor proteins located on
  the surface of B cells and T cells. The REpertoire Sequencing TOolkit
  (pRESTO) is composed of a suite of utilities to handle all stages of
  sequence processing prior to germline segment assignment. pRESTO is
  designed to handle either single reads or paired-end reads. It includes
  features for quality control, primer masking, annotation of reads with
  sequence embedded barcodes, generation of unique molecular identifier
  (UMI) consensus sequences, assembly of paired-end reads and
  identification of duplicate sequences. Numerous options for sequence
  sorting, sampling and conversion operations are also included.

Remark: This package is maintained by Debian Med Packaging Team at

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