Re: New lintian warning: mailing-list-obsolete-in-debian-infrastructure Debian Med Packaging Team
Le Mon, Apr 27, 2020 at 11:52:22AM +0200, Andreas Tille a écrit : > >https://salsa.debian.org/med-team/resfinder/ > > Both versions *.pl and *.py remain in source and it took me a long > time to get an answer from upstream / our users what is really used > and what should be packaged. See also README.Debian. Hi Andreas, thanks a lot for this interesting example. I think that it supports my point of view, because the resfinder.pl and resfinder.py are not drop-in replacements for each other. In particular, they do not support the same set of command-line arguments. In that sense, the Python version looks like a version 2 of the Perl command, without full backwards compatibility. Let's imagine now that we would have renamed `resfinder.pl` to just `resfinder` and that on a package upgrade, we would replace it by a renamed `resfinder.py`. We would just break our users scripts. Have a nice day, Charles -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Akano, Uruma, Okinawa, Japan
Re: Help for asking upstreams about free licenses urgently needed (Was: Help: Seeking source code of guppy base caller)
Hi Andreas and everybody,
I am a regular user of Guppy. We use it to transform ("basecall") raw
signal output from the sequencers manufactured by Oxford Nanopore
Technologies (ONT) to nucleic acid sequence files in the FASTQ format
accepted by many of the tools that we package in Debian Med.
I think that even if ONT would free Guppy, packaging it would be
a significant challlenge.
- Guppy is a moving target, and whichever version we would distribute
in Stable is unlikely to satisfy the users a year later.
- Upgrades are not drop-in replacements for each other and a laboratory
typycally needs to install several versions side-to-side.
- In many cases, a GPU is needed to have Guppy end its computation in
a reasonable time. But Debian does not have an infrastructure to
test GPU computations.
- As far as I know, Guppy is developed on amd64 and arm64 only. We
can therefore expect the usual portability issues.
- The conversion from raw to FASTQ is done by neural network algorithms
for which we do not have access to the training data, and therefore
the freedom to modify Guppy would be limited to the sugar around the
core algorithms.
In that sense, I think that if we want to distribute a basecaller in
Debian, we should better pick an alternative that is already free. Some
of them are reported to perform as well as Guppy. But which one to
pick, and how about long-term mainteance ?
Altogether, I think that we will best serve our users by making sure
that Free basecallers are easy to install on Debian, providing the
standard tools for downstream analysis (we are quite good at this), and
adding value by supporting bioinformatics workflow systems.
Have a nice day,
Charles
--
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Akano, Uruma, Okinawa, Japan
RFS: hunspell-en-med
Hi, I've added autopkgtests to hunspell-en-med. Please review and sponsor. https://salsa.debian.org/med-team/hunspell-en-med Regards, Pranav ᐧ
Re: Help for asking upstreams about free licenses urgently needed (Was: Help: Seeking source code of guppy base caller)
On Sun, May 03, 2020 at 06:05:00PM +0200, Jun Aruga wrote: > Oxford Nanopore Technology's annual event is 18th , 19th June. After > registering your account to attend, you can access some useful > knowledge articles including Guppy on the community site. > https://nanoporetech.com/lc20 Honestly, I do not really want to attend - I want to see free source code to create a Debian package from it. ;-) Thanks for the hint anyway Andreas. -- http://fam-tille.de
Re: Help for asking upstreams about free licenses urgently needed (Was: Help: Seeking source code of guppy base caller)
Oxford Nanopore Technology's annual event is 18th , 19th June. After registering your account to attend, you can access some useful knowledge articles including Guppy on the community site. https://nanoporetech.com/lc20 -- Jun | He - His - Him
