Re: Help for asking upstreams about free licenses urgently needed (Was: Help: Seeking source code of guppy base caller)
- To: Debian Med Project List <email@example.com>
- Subject: Re: Help for asking upstreams about free licenses urgently needed (Was: Help: Seeking source code of guppy base caller)
- From: Andreas Tille <firstname.lastname@example.org>
- Date: Tue, 5 May 2020 06:52:43 +0200
- Message-id: <[🔎] 20200505045243.GI29039@an3as.eu>
- In-reply-to: <[🔎] 20200504013722.GB3214@bubu.plessy.net>
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thanks a lot for your insight.
On Mon, May 04, 2020 at 10:37:22AM +0900, Charles Plessy wrote:
> 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.
I wonder how users of that software are dealing with this.
> - 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.
Regarding this item I would not see any problem. We can easily restrict
the architectures as well.
> - 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.
That's a strong point actually. However, we will face more and more
problems of this nature. Mo's attempt to write a deep learning policy
might help here a bit.
> 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 ?
Once I've started packaging deepbinner which is stalled as long as we
do not have python3-tensorflow. But may be that's at the horizon since
bazel packaging sounded quite promising.
> 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.
That's exactly my opinion here.