Idea wanted: What is the most key open source projects to fight COVID-19?

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Idea wanted: What is the most key open source projects to fight COVID-19?

Jun Aruga-2
Watching COVID19 Virtual BioHackathon 2020 kick-off [1] and wrap-up
[2] videos, I was thinking about this question.

What are the most key open source projects (or packages) that we need
to care to maintain to fight COVID-19?

"key" means the packages that we care more about than other packages.
Sorry for the ambiguous question.
I am curious and want to be concious about the priorities.

Well, it's a broader topic. There are several factors such as
Sequencing, Machine Learning, Graph, Workflow and etc in it.
I shared the 3 nf-core pipelines nf-core/nanoseq, nf-core/artic,
nf-core/viralrecon in the email thread: Subject
https://github.com/nf-core/covid19 - nextflow pipeline . And the
following are the used software in each pipeline.

In my option, the packages written in compiling language such as C,
C++ and taking long time to compile are the "key" packages. Because
users can still run the script language software without deb package,
and users can compile software that is easy to compile by themselves.
And the essential function's software is also the key. In this case,
that is sequencing aligner.

So, the key packages are bowite2, minimap2, bwa in the list of the pipelines.
And simde is used to support the packages on multiple CPU architctures [3].

So, the most key packages that we care about to fight COVID-19 are in
order to the priority.

1. simde
2. bowtie2 (build time is long. It's relatively hard to compile it).
3. minimap2
4. bwa

That's my observation.
So, do you have any ideas or observations about the question? I would
like to hear.

Thank you.

## Used software in each pipeline.

https://github.com/nf-core/nanoseq/blob/master/bin/scrape_software_versions.py
guppy
qcat
pycoQC
NanoPlot'
FastQC
GraphMap2
minimap2
Samtools
BEDTools
MultiQC'

https://github.com/nf-core/artic/blob/dev/bin/scrape_software_versions.py
FastQC
NanoPlot
BWA
minimap2
Samtools
BEDTools
MultiQC

https://github.com/nf-core/viralrecon/blob/dev/bin/scrape_software_versions.py
parallel-fastq-dump
FastQC
fastp
Bowtie 2
Samtools
BEDTools
Picard
iVar
VarScan 2
SnpEff
SnpSift'
BCFTools
Cutadapt
Kraken2
SPAdes
Unicycler
minia
Minimap2
vg
BLAST
ABACAS
QUAST
R
MultiQC'

[1] https://youtu.be/x-QTP5Z_WIU
[2] https://youtu.be/g5cQk8jIMwo
[3] https://wiki.debian.org/SIMDEverywhere

--
Jun | He - His - Him

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Re: Idea wanted: What is the most key open source projects to fight COVID-19?

Andreas Tille-5
Dear Jun,

On Tue, Apr 21, 2020 at 10:47:09PM +0200, Jun Aruga wrote:

> Watching COVID19 Virtual BioHackathon 2020 kick-off [1] and wrap-up
> [2] videos, I was thinking about this question.
>
> What are the most key open source projects (or packages) that we need
> to care to maintain to fight COVID-19?
>
> "key" means the packages that we care more about than other packages.
> Sorry for the ambiguous question.
> I am curious and want to be concious about the priorities.
>
> Well, it's a broader topic. There are several factors such as
> Sequencing, Machine Learning, Graph, Workflow and etc in it.
> I shared the 3 nf-core pipelines nf-core/nanoseq, nf-core/artic,
> nf-core/viralrecon in the email thread: Subject
> https://github.com/nf-core/covid19 - nextflow pipeline . And the
> following are the used software in each pipeline.

Thank you for this analysis.

> In my option, the packages written in compiling language such as C,
> C++ and taking long time to compile are the "key" packages.

I personally would not subscribe the distinction based on the technology
used to develop the software.  I'd rather decide on the pure usage
statistics.  Sometimes the dependency tree is pretty complex and packages
of interpreted languages might get in conflict.  IMHO its better to
priorise on
   a) function
   b) available tests

> Because
> users can still run the script language software without deb package,
> and users can compile software that is easy to compile by themselves.
> And the essential function's software is also the key. In this case,
> that is sequencing aligner.
>
> So, the key packages are bowite2, minimap2, bwa in the list of the pipelines.
> And simde is used to support the packages on multiple CPU architctures [3].
>
> So, the most key packages that we care about to fight COVID-19 are in
> order to the priority.
>
> 1. simde
> 2. bowtie2 (build time is long. It's relatively hard to compile it).
> 3. minimap2
> 4. bwa

I'm lacking the bioinformatics background to decide about this but from
usage numbers these packages seem to be frequently used.
 
> That's my observation.
> So, do you have any ideas or observations about the question? I would
> like to hear.
>
> Thank you.
>
> ## Used software in each pipeline.


I'm adding comments to the software packages you mentioned:
 
> https://github.com/nf-core/nanoseq/blob/master/bin/scrape_software_versions.py
> guppy
Missing in Debian.  Is it this project
   https://staff.aist.go.jp/yutaka.ueno/guppy/  ?

> qcat
> pycoQC
Both just uploaded to new (including dependency python3-parasail)

> NanoPlot
I'll add
   https://github.com/wdecoster/NanoPlot
to our todo list

> FastQC
In Debian.

> GraphMap2
I'll add
   https://github.com/lbcb-sci/graphmap2
to our todo list

> minimap2
> Samtools
> BEDTools
> MultiQC
All four in Debian.

>
> https://github.com/nf-core/artic/blob/dev/bin/scrape_software_versions.py
> FastQC
> NanoPlot
> BWA
> minimap2
> Samtools
> BEDTools
> MultiQC

See above regarding NanoPlot - all others in Debian.

>
> https://github.com/nf-core/viralrecon/blob/dev/bin/scrape_software_versions.py
> parallel-fastq-dump
I'll add
   https://github.com/rvalieris/parallel-fastq-dump
to our todo list

> FastQC
> fastp
> Bowtie 2
> Samtools
> BEDTools
> Picard
All in Debian.

> iVar
I'll add
   https://github.com/andersen-lab/ivar
to our todo list

> VarScan 2
In Debian non-free.  Its on our software liberation Wiki
   https://wiki.debian.org/DebianMed/SoftwareLiberation
   It would be a *huge* service to the community to
   convince upstream about free license
 
> SnpEff
Ahhhh, that one rings a bell.  Its hard since several not yet packaged
predepends.  I've spent hours on it before but I'll add this to our
todo list
   https://salsa.debian.org/med-team/snpeff

> SnpSift
Same source as SnpEff (see above)

> BCFTools
> Cutadapt
> Kraken2
> SPAdes
> Unicycler
> minia
> Minimap2
> vg
> BLAST
> ABACAS
All in Debian.

> QUAST

Thats a pretty complex assembly of third party software (for instance
including their own copy of bwa, minimap2, bedtools and lots of others).
For instance it was my motivation to package sambamba which on its own
is quite a complex packaging project (beeing RC buggy half of the time
of its existance :-().  It also includes genemark a binary since it is
non-free - see again our software liberation page
   https://wiki.debian.org/DebianMed/SoftwareLiberation
   -> I'd like to repeat that freeing this would be very sensible.
In short packaging quast is pretty tough - but there is at least a
weak (not building yet!) start:
   https://salsa.debian.org/med-team/quast

> R

Well R in itself is cheap - if some specific R packages are used and
we might not have packaged these this should be easily doable.

> MultiQC
In Debian.


In general your list of software is extremely helpful.  Thanks a lot for
it.  I've added it to the covid-19 task[4] (which will be re-rendered
soon).  The said todo list were I've added the projects is in the COVID-19
coordination wiki[5]

As always: Everybody is kindly invited to pick from the todo list.
Please do not underestimate the todo items contacting authors to free
their code.  Every little contribution here is *extremely* helpful and
highly appreciated.

Thanks again Jun for your very helpful contribution

     Andreas.

> [1] https://youtu.be/x-QTP5Z_WIU
> [2] https://youtu.be/g5cQk8jIMwo
> [3] https://wiki.debian.org/SIMDEverywhere
[4] https://blends.debian.org/med/tasks/covid-19
[5] https://salsa.debian.org/med-team/community/2020-covid19-hackathon/-/wikis/COVID-19-Hackathon-packages-needing-work

--
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Re: Idea wanted: What is the most key open source projects to fight COVID-19?

Jun Aruga-2
> > https://github.com/nf-core/nanoseq/blob/master/bin/scrape_software_versions.py
> > guppy
> Missing in Debian.  Is it this project
>    https://staff.aist.go.jp/yutaka.ueno/guppy/  ?

Hi, Andreas,
No, it seems that guppy is a base caller provided by Oxford Nanopore
technologies.

```
$ pwd
/home/jaruga/git/nf-core/nanoseq

$ grep -r guppy *
...
conf/base.config:      container = 'genomicpariscentre/guppy-gpu:3.4.4'
conf/base.config:      container = 'genomicpariscentre/guppy:3.4.4'
...

Then check the containers Dockerfile.

https://hub.docker.com/r/genomicpariscentre/guppy/dockerfile
> wget -q https://mirror.oxfordnanoportal.com/software/analysis/ont_guppy_cpu_${PACKAGE_VERSION}-1~xenial_amd64.deb

https://hub.docker.com/r/genomicpariscentre/guppy-gpu/dockerfile
> wget -q https://mirror.oxfordnanoportal.com/software/analysis/ont_guppy_${PACKAGE_VERSION}-1~xenial_amd64.deb
```

It might not be open source software, seeing the following page.
Here is a user's page about guppy in Japanese. I could not find the
English page.
You can see the guppy's screen shot on
https://community.nanoporetech.com/downloads page.

http://kazumaxneo.hatenablog.com/entry/2020/01/19/145940

> Thanks again Jun for your very helpful contribution

You are welcome. Let me comment on your comments later.

Cheers,
Jun

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Jun | He - His - Him

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Help: Seeking source code of guppy base caller (Was: Idea wanted: What is the most key open source projects to fight COVID-19?)

Andreas Tille-2
Hi,

I also tried my luck to find the source code for guppy base caller - but
failed.  It would of great help if somebody could find out.

Thanks a lot Jun for giving detailed hints so far

     Andreas.

On Fri, Apr 24, 2020 at 08:41:22PM +0200, Jun Aruga wrote:

> > > https://github.com/nf-core/nanoseq/blob/master/bin/scrape_software_versions.py
> > > guppy
> > Missing in Debian.  Is it this project
> >    https://staff.aist.go.jp/yutaka.ueno/guppy/  ?
>
> Hi, Andreas,
> No, it seems that guppy is a base caller provided by Oxford Nanopore
> technologies.
>
> ```
> $ pwd
> /home/jaruga/git/nf-core/nanoseq
>
> $ grep -r guppy *
> ...
> conf/base.config:      container = 'genomicpariscentre/guppy-gpu:3.4.4'
> conf/base.config:      container = 'genomicpariscentre/guppy:3.4.4'
> ...
>
> Then check the containers Dockerfile.
>
> https://hub.docker.com/r/genomicpariscentre/guppy/dockerfile
> > wget -q https://mirror.oxfordnanoportal.com/software/analysis/ont_guppy_cpu_${PACKAGE_VERSION}-1~xenial_amd64.deb
>
> https://hub.docker.com/r/genomicpariscentre/guppy-gpu/dockerfile
> > wget -q https://mirror.oxfordnanoportal.com/software/analysis/ont_guppy_${PACKAGE_VERSION}-1~xenial_amd64.deb
> ```
>
> It might not be open source software, seeing the following page.
> Here is a user's page about guppy in Japanese. I could not find the
> English page.
> You can see the guppy's screen shot on
> https://community.nanoporetech.com/downloads page.
>
> http://kazumaxneo.hatenablog.com/entry/2020/01/19/145940
>
> > Thanks again Jun for your very helpful contribution
>
> You are welcome. Let me comment on your comments later.
>
> Cheers,
> Jun
>
> --
> Jun | He - His - Him
>
>

--
http://fam-tille.de

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Re: Help: Seeking source code of guppy base caller (Was: Idea wanted: What is the most key open source projects to fight COVID-19?)

Michael Crusoe
Extracting the linked deb, one finds a binary and a very restrictive license. I do not believe that guppy source code is available nor it is likely to become available any time soon.

While some of their other basecallers have source code available, I would not call the license OSS: https://github.com/nanoporetech/flappie/blob/master/LICENCE.txt



On Mon, Apr 27, 2020 at 2:58 PM Andreas Tille <[hidden email]> wrote:
Hi,

I also tried my luck to find the source code for guppy base caller - but
failed.  It would of great help if somebody could find out.

Thanks a lot Jun for giving detailed hints so far

     Andreas.

On Fri, Apr 24, 2020 at 08:41:22PM +0200, Jun Aruga wrote:
> > > https://github.com/nf-core/nanoseq/blob/master/bin/scrape_software_versions.py
> > > guppy
> > Missing in Debian.  Is it this project
> >    https://staff.aist.go.jp/yutaka.ueno/guppy/  ?
>
> Hi, Andreas,
> No, it seems that guppy is a base caller provided by Oxford Nanopore
> technologies.
>
> ```
> $ pwd
> /home/jaruga/git/nf-core/nanoseq
>
> $ grep -r guppy *
> ...
> conf/base.config:      container = 'genomicpariscentre/guppy-gpu:3.4.4'
> conf/base.config:      container = 'genomicpariscentre/guppy:3.4.4'
> ...
>
> Then check the containers Dockerfile.
>
> https://hub.docker.com/r/genomicpariscentre/guppy/dockerfile
> > wget -q https://mirror.oxfordnanoportal.com/software/analysis/ont_guppy_cpu_${PACKAGE_VERSION}-1~xenial_amd64.deb
>
> https://hub.docker.com/r/genomicpariscentre/guppy-gpu/dockerfile
> > wget -q https://mirror.oxfordnanoportal.com/software/analysis/ont_guppy_${PACKAGE_VERSION}-1~xenial_amd64.deb
> ```
>
> It might not be open source software, seeing the following page.
> Here is a user's page about guppy in Japanese. I could not find the
> English page.
> You can see the guppy's screen shot on
> https://community.nanoporetech.com/downloads page.
>
> http://kazumaxneo.hatenablog.com/entry/2020/01/19/145940
>
> > Thanks again Jun for your very helpful contribution
>
> You are welcome. Let me comment on your comments later.
>
> Cheers,
> Jun
>
> --
> Jun | He - His - Him
>
>

--
http://fam-tille.de



--
Michael R. Crusoe
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Help for asking upstreams about free licenses urgently needed (Was: Help: Seeking source code of guppy base caller)

Andreas Tille-2
Hi again,

this brings up again my point: We *really*, *really* should take the
chance right now to ask upstreams for free licensing.  The time is good.
We just need somebody who is really doing this.

Kind regards

       Andreas.

On Mon, Apr 27, 2020 at 04:21:12PM +0200, Michael Crusoe wrote:

> Extracting the linked deb, one finds a binary and a very restrictive
> license. I do not believe that guppy source code is available nor it is
> likely to become available any time soon.
>
> While some of their other basecallers have source code available, I would
> not call the license OSS:
> https://github.com/nanoporetech/flappie/blob/master/LICENCE.txt
>
>
>
> On Mon, Apr 27, 2020 at 2:58 PM Andreas Tille <[hidden email]> wrote:
>
> > Hi,
> >
> > I also tried my luck to find the source code for guppy base caller - but
> > failed.  It would of great help if somebody could find out.
> >
> > Thanks a lot Jun for giving detailed hints so far
> >
> >      Andreas.
> >
> > On Fri, Apr 24, 2020 at 08:41:22PM +0200, Jun Aruga wrote:
> > > > >
> > https://github.com/nf-core/nanoseq/blob/master/bin/scrape_software_versions.py
> > > > > guppy
> > > > Missing in Debian.  Is it this project
> > > >    https://staff.aist.go.jp/yutaka.ueno/guppy/  ?
> > >
> > > Hi, Andreas,
> > > No, it seems that guppy is a base caller provided by Oxford Nanopore
> > > technologies.
> > >
> > > ```
> > > $ pwd
> > > /home/jaruga/git/nf-core/nanoseq
> > >
> > > $ grep -r guppy *
> > > ...
> > > conf/base.config:      container = 'genomicpariscentre/guppy-gpu:3.4.4'
> > > conf/base.config:      container = 'genomicpariscentre/guppy:3.4.4'
> > > ...
> > >
> > > Then check the containers Dockerfile.
> > >
> > > https://hub.docker.com/r/genomicpariscentre/guppy/dockerfile
> > > > wget -q
> > https://mirror.oxfordnanoportal.com/software/analysis/ont_guppy_cpu_${PACKAGE_VERSION}-1~xenial_amd64.deb
> > >
> > > https://hub.docker.com/r/genomicpariscentre/guppy-gpu/dockerfile
> > > > wget -q
> > https://mirror.oxfordnanoportal.com/software/analysis/ont_guppy_${PACKAGE_VERSION}-1~xenial_amd64.deb
> > > ```
> > >
> > > It might not be open source software, seeing the following page.
> > > Here is a user's page about guppy in Japanese. I could not find the
> > > English page.
> > > You can see the guppy's screen shot on
> > > https://community.nanoporetech.com/downloads page.
> > >
> > > http://kazumaxneo.hatenablog.com/entry/2020/01/19/145940
> > >
> > > > Thanks again Jun for your very helpful contribution
> > >
> > > You are welcome. Let me comment on your comments later.
> > >
> > > Cheers,
> > > Jun
> > >
> > > --
> > > Jun | He - His - Him
> > >
> > >
> >
> > --
> > http://fam-tille.de
> >
> >
>
> --
> Michael R. Crusoe

--
http://fam-tille.de

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Re: Help for asking upstreams about free licenses urgently needed (Was: Help: Seeking source code of guppy base caller)

Jun Aruga-2
On Mon, Apr 27, 2020 at 4:43 PM Andreas Tille <[hidden email]> wrote:
>
> Hi again,
>
> this brings up again my point: We *really*, *really* should take the
> chance right now to ask upstreams for free licensing.  The time is good.
> We just need somebody who is really doing this.

For us, the free licensing is good. But for the company nanopore
technologies it is their core competency.
I am not sure we can make it happen, but it might be worth trying to ask.

> On Mon, Apr 27, 2020 at 04:21:12PM +0200, Michael Crusoe wrote:
> > Extracting the linked deb, one finds a binary and a very restrictive
> > license. I do not believe that guppy source code is available nor it is
> > likely to become available any time soon.
> >
> > While some of their other basecallers have source code available, I would
> > not call the license OSS:
> > https://github.com/nanoporetech/flappie/blob/master/LICENCE.txt

I found guppy client software that might be an alternative to use
guppy's function.
https://github.com/nanoporetech/pyguppyclient

As Michael mentioned, checking other basecallers for nanopore, then
communicating the nf-core/nanoseq project using the alternative base
caller optionally.

I found an interesting document about the basecallers.
https://github.com/rrwick/Basecalling-comparison

Performance of neural network basecalling tools for Oxford Nanopore sequencing
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1727-y

> In this study, we tested four basecalling programs developed by ONT – Albacore, Guppy, Scrappie and Flappie
> ...
> We also tested Chiron (https://github.com/haotianteng/Chiron), a third-party basecaller still under development that uses a deeper neural network than ONT’s basecallers [3].

The third party basecaller Chiron's license is Mozilla Public License, v. 2.0.
https://github.com/haotianteng/Chiron/blob/master/LICENSE.md

--
Jun | He - His - Him

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Re: Help for asking upstreams about free licenses urgently needed (Was: Help: Seeking source code of guppy base caller)

Andreas Tille-5
Hi Jun,

On Mon, Apr 27, 2020 at 05:06:41PM +0200, Jun Aruga wrote:
> > this brings up again my point: We *really*, *really* should take the
> > chance right now to ask upstreams for free licensing.  The time is good.
> > We just need somebody who is really doing this.
>
> For us, the free licensing is good. But for the company nanopore
> technologies it is their core competency.
> I am not sure we can make it happen, but it might be worth trying to ask.

That's what I mean:  Just lets ask (not only in this case but also
in others).  There are always good arguments for Open Source and
if nobody asks we will not reach anything.  As you can see here

   https://wiki.debian.org/DebianMed/SoftwareLiberation

our (partly continuous asking) had quite some success.  With COVID-19 we
have one more good reason to ask.  I'm simply lacking time and energy to
do *all* this.
 

> > On Mon, Apr 27, 2020 at 04:21:12PM +0200, Michael Crusoe wrote:
> > > Extracting the linked deb, one finds a binary and a very restrictive
> > > license. I do not believe that guppy source code is available nor it is
> > > likely to become available any time soon.
> > >
> > > While some of their other basecallers have source code available, I would
> > > not call the license OSS:
> > > https://github.com/nanoporetech/flappie/blob/master/LICENCE.txt
>
> I found guppy client software that might be an alternative to use
> guppy's function.
> https://github.com/nanoporetech/pyguppyclient

I have not checked but isn't this just a Python interface to guppy?
 
> As Michael mentioned, checking other basecallers for nanopore, then
> communicating the nf-core/nanoseq project using the alternative base
> caller optionally.
>
> I found an interesting document about the basecallers.
> https://github.com/rrwick/Basecalling-comparison

I've also found this one.
 
> Performance of neural network basecalling tools for Oxford Nanopore sequencing
> https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1727-y
>
> > In this study, we tested four basecalling programs developed by ONT – Albacore, Guppy, Scrappie and Flappie
> > ...
> > We also tested Chiron (https://github.com/haotianteng/Chiron), a third-party basecaller still under development that uses a deeper neural network than ONT’s basecallers [3].
>
> The third party basecaller Chiron's license is Mozilla Public License, v. 2.0.
> https://github.com/haotianteng/Chiron/blob/master/LICENSE.md

I have no idea whether we can make this a drop in replacement.
But may be its interesting in any case.

Kind regards

       Andreas.

--
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Re: Help for asking upstreams about free licenses urgently needed (Was: Help: Seeking source code of guppy base caller)

Ben Tris
In reply to this post by Jun Aruga-2
Sorry to pop in.
I think this license should be reviewed,
unless sure it is not a free license.
To me it looks like a free software license.
Although not understand most.

What is making this license non-free?

On 27-04-20 17:06, Jun Aruga wrote:

> On Mon, Apr 27, 2020 at 4:43 PM Andreas Tille <[hidden email]> wrote:
>> Hi again,
>>
>> this brings up again my point: We *really*, *really* should take the
>> chance right now to ask upstreams for free licensing.  The time is good.
>> We just need somebody who is really doing this.
> For us, the free licensing is good. But for the company nanopore
> technologies it is their core competency.
> I am not sure we can make it happen, but it might be worth trying to ask.
>
>> On Mon, Apr 27, 2020 at 04:21:12PM +0200, Michael Crusoe wrote:
>>> Extracting the linked deb, one finds a binary and a very restrictive
>>> license. I do not believe that guppy source code is available nor it is
>>> likely to become available any time soon.
>>>
>>> While some of their other basecallers have source code available, I would
>>> not call the license OSS:
>>> https://github.com/nanoporetech/flappie/blob/master/LICENCE.txt
> I found guppy client software that might be an alternative to use
> guppy's function.
> https://github.com/nanoporetech/pyguppyclient
>
> As Michael mentioned, checking other basecallers for nanopore, then
> communicating the nf-core/nanoseq project using the alternative base
> caller optionally.
>
> I found an interesting document about the basecallers.
> https://github.com/rrwick/Basecalling-comparison
>
> Performance of neural network basecalling tools for Oxford Nanopore sequencing
> https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1727-y
>
>> In this study, we tested four basecalling programs developed by ONT – Albacore, Guppy, Scrappie and Flappie
>> ...
>> We also tested Chiron (https://github.com/haotianteng/Chiron), a third-party basecaller still under development that uses a deeper neural network than ONT’s basecallers [3].
> The third party basecaller Chiron's license is Mozilla Public License, v. 2.0.
> https://github.com/haotianteng/Chiron/blob/master/LICENSE.md
>


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Re: Help for asking upstreams about free licenses urgently needed (Was: Help: Seeking source code of guppy base caller)

Andreas Tille-5
On Mon, Apr 27, 2020 at 06:39:44PM +0200, Ben Tris wrote:
> Sorry to pop in.
> I think this license should be reviewed,

What exact license are you talking about.  I'm missing a link
to guppy source code including any license.

> unless sure it is not a free license.
> To me it looks like a free software license.

Which one are you talking about?

Kind regards

      Andreas.

> Although not understand most.
>
> What is making this license non-free?
>
> On 27-04-20 17:06, Jun Aruga wrote:
> > On Mon, Apr 27, 2020 at 4:43 PM Andreas Tille <[hidden email]> wrote:
> >> Hi again,
> >>
> >> this brings up again my point: We *really*, *really* should take the
> >> chance right now to ask upstreams for free licensing.  The time is good.
> >> We just need somebody who is really doing this.
> > For us, the free licensing is good. But for the company nanopore
> > technologies it is their core competency.
> > I am not sure we can make it happen, but it might be worth trying to ask.
> >
> >> On Mon, Apr 27, 2020 at 04:21:12PM +0200, Michael Crusoe wrote:
> >>> Extracting the linked deb, one finds a binary and a very restrictive
> >>> license. I do not believe that guppy source code is available nor it is
> >>> likely to become available any time soon.
> >>>
> >>> While some of their other basecallers have source code available, I would
> >>> not call the license OSS:
> >>> https://github.com/nanoporetech/flappie/blob/master/LICENCE.txt
> > I found guppy client software that might be an alternative to use
> > guppy's function.
> > https://github.com/nanoporetech/pyguppyclient
> >
> > As Michael mentioned, checking other basecallers for nanopore, then
> > communicating the nf-core/nanoseq project using the alternative base
> > caller optionally.
> >
> > I found an interesting document about the basecallers.
> > https://github.com/rrwick/Basecalling-comparison
> >
> > Performance of neural network basecalling tools for Oxford Nanopore sequencing
> > https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1727-y
> >
> >> In this study, we tested four basecalling programs developed by ONT – Albacore, Guppy, Scrappie and Flappie
> >> ...
> >> We also tested Chiron (https://github.com/haotianteng/Chiron), a third-party basecaller still under development that uses a deeper neural network than ONT’s basecallers [3].
> > The third party basecaller Chiron's license is Mozilla Public License, v. 2.0.
> > https://github.com/haotianteng/Chiron/blob/master/LICENSE.md
> >
>




--
http://fam-tille.de

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Re: Help for asking upstreams about free licenses urgently needed (Was: Help: Seeking source code of guppy base caller)

Michael Crusoe
In reply to this post by Ben Tris
No source code is provided. No competitors of the company may use the software. Must be for "research use only".

https://github.com/nanoporetech/flappie/blob/master/LICENCE.txt 
"Oxford Nanopore Technologies, Ltd. Public License Version 1.0" is used to license some of their "source available" software
Only permits "research purposes", violating DFSG guideline #6 "No Discrimination Against Fields of Endeavor"

https://github.com/haotianteng/Chiron/blob/master/LICENSE.md is the Mozilla Public License and is DFSG compatible

On Mon, Apr 27, 2020 at 6:40 PM Ben Tris <[hidden email]> wrote:
Sorry to pop in.
I think this license should be reviewed,
unless sure it is not a free license.
To me it looks like a free software license.
Although not understand most.

What is making this license non-free?

On 27-04-20 17:06, Jun Aruga wrote:
> On Mon, Apr 27, 2020 at 4:43 PM Andreas Tille <[hidden email]> wrote:
>> Hi again,
>>
>> this brings up again my point: We *really*, *really* should take the
>> chance right now to ask upstreams for free licensing.  The time is good.
>> We just need somebody who is really doing this.
> For us, the free licensing is good. But for the company nanopore
> technologies it is their core competency.
> I am not sure we can make it happen, but it might be worth trying to ask.
>
>> On Mon, Apr 27, 2020 at 04:21:12PM +0200, Michael Crusoe wrote:
>>> Extracting the linked deb, one finds a binary and a very restrictive
>>> license. I do not believe that guppy source code is available nor it is
>>> likely to become available any time soon.
>>>
>>> While some of their other basecallers have source code available, I would
>>> not call the license OSS:
>>> https://github.com/nanoporetech/flappie/blob/master/LICENCE.txt
> I found guppy client software that might be an alternative to use
> guppy's function.
> https://github.com/nanoporetech/pyguppyclient
>
> As Michael mentioned, checking other basecallers for nanopore, then
> communicating the nf-core/nanoseq project using the alternative base
> caller optionally.
>
> I found an interesting document about the basecallers.
> https://github.com/rrwick/Basecalling-comparison
>
> Performance of neural network basecalling tools for Oxford Nanopore sequencing
> https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1727-y
>
>> In this study, we tested four basecalling programs developed by ONT – Albacore, Guppy, Scrappie and Flappie
>> ...
>> We also tested Chiron (https://github.com/haotianteng/Chiron), a third-party basecaller still under development that uses a deeper neural network than ONT’s basecallers [3].
> The third party basecaller Chiron's license is Mozilla Public License, v. 2.0.
> https://github.com/haotianteng/Chiron/blob/master/LICENSE.md
>



--
Michael R. Crusoe
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Re: Help for asking upstreams about free licenses urgently needed (Was: Help: Seeking source code of guppy base caller)

Andreas Tille-2
Hi Michael,

thanks a lot for the links.  Any volunteer to start some discussion?
As I said:  If we do not try nothing will change.  People with no
technical skills could contribute by doing so to take some workload
from packagers.

I'll offer a $DRINK at next Debian Med sprint for every attempt to
change a license. ;-)

Kind regards

      Andreas.

On Tue, Apr 28, 2020 at 09:30:06AM +0200, Michael Crusoe wrote:

> The guppy binary license is
> https://nanoporetech.com/sites/default/files/s3/terms/Nanopore-product-terms-and-conditions-nov2018-v2.pdf
> No source code is provided. No competitors of the company may use the
> software. Must be for "research use only".
>
> https://github.com/nanoporetech/flappie/blob/master/LICENCE.txt
> "Oxford Nanopore Technologies, Ltd. Public License Version 1.0" is used to
> license some of their "source available" software
> Only permits "research purposes", violating DFSG guideline #6 "No
> Discrimination Against Fields of Endeavor"
>
> https://github.com/haotianteng/Chiron/blob/master/LICENSE.md is the Mozilla
> Public License and is DFSG compatible
>
> On Mon, Apr 27, 2020 at 6:40 PM Ben Tris <[hidden email]> wrote:
>
> > Sorry to pop in.
> > I think this license should be reviewed,
> > unless sure it is not a free license.
> > To me it looks like a free software license.
> > Although not understand most.
> >
> > What is making this license non-free?
> >
> > On 27-04-20 17:06, Jun Aruga wrote:
> > > On Mon, Apr 27, 2020 at 4:43 PM Andreas Tille <[hidden email]> wrote:
> > >> Hi again,
> > >>
> > >> this brings up again my point: We *really*, *really* should take the
> > >> chance right now to ask upstreams for free licensing.  The time is good.
> > >> We just need somebody who is really doing this.
> > > For us, the free licensing is good. But for the company nanopore
> > > technologies it is their core competency.
> > > I am not sure we can make it happen, but it might be worth trying to ask.
> > >
> > >> On Mon, Apr 27, 2020 at 04:21:12PM +0200, Michael Crusoe wrote:
> > >>> Extracting the linked deb, one finds a binary and a very restrictive
> > >>> license. I do not believe that guppy source code is available nor it is
> > >>> likely to become available any time soon.
> > >>>
> > >>> While some of their other basecallers have source code available, I
> > would
> > >>> not call the license OSS:
> > >>> https://github.com/nanoporetech/flappie/blob/master/LICENCE.txt
> > > I found guppy client software that might be an alternative to use
> > > guppy's function.
> > > https://github.com/nanoporetech/pyguppyclient
> > >
> > > As Michael mentioned, checking other basecallers for nanopore, then
> > > communicating the nf-core/nanoseq project using the alternative base
> > > caller optionally.
> > >
> > > I found an interesting document about the basecallers.
> > > https://github.com/rrwick/Basecalling-comparison
> > >
> > > Performance of neural network basecalling tools for Oxford Nanopore
> > sequencing
> > >
> > https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1727-y
> > >
> > >> In this study, we tested four basecalling programs developed by ONT –
> > Albacore, Guppy, Scrappie and Flappie
> > >> ...
> > >> We also tested Chiron (https://github.com/haotianteng/Chiron), a
> > third-party basecaller still under development that uses a deeper neural
> > network than ONT’s basecallers [3].
> > > The third party basecaller Chiron's license is Mozilla Public License,
> > v. 2.0.
> > > https://github.com/haotianteng/Chiron/blob/master/LICENSE.md
> > >
> >
> >
>
> --
> Michael R. Crusoe

--
http://fam-tille.de

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Re: Help for asking upstreams about free licenses urgently needed (Was: Help: Seeking source code of guppy base caller)

Ben Tris
I was referring to the flappy license, that is mozilla like
maybe they are willing to change to MPL-2.0 that is GPL compatible
if that research only is a problem, but I think (guess) there are
enough escapes in the license.

I still think there should be a confirmation
that guppy will not be available with a free software
license. Because I think it is developed with
contributions from the community.

Otherwise it is indeed non-free.

Based on the flappy license, should asked to release guppy with MPL-2.0?

Someone mentioned chiron, maybe that is the only good alternative at
this moment?
(the Basecalling-comparison contains some additional advice on chiron
settings)

On 28-04-20 10:11, Andreas Tille wrote:

> Hi Michael,
>
> thanks a lot for the links.  Any volunteer to start some discussion?
> As I said:  If we do not try nothing will change.  People with no
> technical skills could contribute by doing so to take some workload
> from packagers.
>
> I'll offer a $DRINK at next Debian Med sprint for every attempt to
> change a license. ;-)
>
> Kind regards
>
>       Andreas.
>
> On Tue, Apr 28, 2020 at 09:30:06AM +0200, Michael Crusoe wrote:
>> The guppy binary license is
>> https://nanoporetech.com/sites/default/files/s3/terms/Nanopore-product-terms-and-conditions-nov2018-v2.pdf
>> No source code is provided. No competitors of the company may use the
>> software. Must be for "research use only".
>>
>> https://github.com/nanoporetech/flappie/blob/master/LICENCE.txt
>> "Oxford Nanopore Technologies, Ltd. Public License Version 1.0" is used to
>> license some of their "source available" software
>> Only permits "research purposes", violating DFSG guideline #6 "No
>> Discrimination Against Fields of Endeavor"
>>
>> https://github.com/haotianteng/Chiron/blob/master/LICENSE.md is the Mozilla
>> Public License and is DFSG compatible
>>
>> On Mon, Apr 27, 2020 at 6:40 PM Ben Tris <[hidden email]> wrote:
>>
>>> Sorry to pop in.
>>> I think this license should be reviewed,
>>> unless sure it is not a free license.
>>> To me it looks like a free software license.
>>> Although not understand most.
>>>
>>> What is making this license non-free?
>>>
>>> On 27-04-20 17:06, Jun Aruga wrote:
>>>> On Mon, Apr 27, 2020 at 4:43 PM Andreas Tille <[hidden email]> wrote:
>>>>> Hi again,
>>>>>
>>>>> this brings up again my point: We *really*, *really* should take the
>>>>> chance right now to ask upstreams for free licensing.  The time is good.
>>>>> We just need somebody who is really doing this.
>>>> For us, the free licensing is good. But for the company nanopore
>>>> technologies it is their core competency.
>>>> I am not sure we can make it happen, but it might be worth trying to ask.
>>>>
>>>>> On Mon, Apr 27, 2020 at 04:21:12PM +0200, Michael Crusoe wrote:
>>>>>> Extracting the linked deb, one finds a binary and a very restrictive
>>>>>> license. I do not believe that guppy source code is available nor it is
>>>>>> likely to become available any time soon.
>>>>>>
>>>>>> While some of their other basecallers have source code available, I
>>> would
>>>>>> not call the license OSS:
>>>>>> https://github.com/nanoporetech/flappie/blob/master/LICENCE.txt
>>>> I found guppy client software that might be an alternative to use
>>>> guppy's function.
>>>> https://github.com/nanoporetech/pyguppyclient
>>>>
>>>> As Michael mentioned, checking other basecallers for nanopore, then
>>>> communicating the nf-core/nanoseq project using the alternative base
>>>> caller optionally.
>>>>
>>>> I found an interesting document about the basecallers.
>>>> https://github.com/rrwick/Basecalling-comparison
>>>>
>>>> Performance of neural network basecalling tools for Oxford Nanopore
>>> sequencing
>>> https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1727-y
>>>>> In this study, we tested four basecalling programs developed by ONT –
>>> Albacore, Guppy, Scrappie and Flappie
>>>>> ...
>>>>> We also tested Chiron (https://github.com/haotianteng/Chiron), a
>>> third-party basecaller still under development that uses a deeper neural
>>> network than ONT’s basecallers [3].
>>>> The third party basecaller Chiron's license is Mozilla Public License,
>>> v. 2.0.
>>>> https://github.com/haotianteng/Chiron/blob/master/LICENSE.md
>>>>
>>>
>> --
>> Michael R. Crusoe


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Re: Help for asking upstreams about free licenses urgently needed (Was: Help: Seeking source code of guppy base caller)

Andreas Tille-6
Hi Ben,

would you volunteer to contact the authors about this?

Thanks a lot in advance

      Andreas.

On Tue, Apr 28, 2020 at 03:01:51PM +0200, Ben Tris wrote:

> I was referring to the flappy license, that is mozilla like
> maybe they are willing to change to MPL-2.0 that is GPL compatible
> if that research only is a problem, but I think (guess) there are
> enough escapes in the license.
>
> I still think there should be a confirmation
> that guppy will not be available with a free software
> license. Because I think it is developed with
> contributions from the community.
>
> Otherwise it is indeed non-free.
>
> Based on the flappy license, should asked to release guppy with MPL-2.0?
>
> Someone mentioned chiron, maybe that is the only good alternative at
> this moment?
> (the Basecalling-comparison contains some additional advice on chiron
> settings)
>
> On 28-04-20 10:11, Andreas Tille wrote:
> > Hi Michael,
> >
> > thanks a lot for the links.  Any volunteer to start some discussion?
> > As I said:  If we do not try nothing will change.  People with no
> > technical skills could contribute by doing so to take some workload
> > from packagers.
> >
> > I'll offer a $DRINK at next Debian Med sprint for every attempt to
> > change a license. ;-)
> >
> > Kind regards
> >
> >       Andreas.
> >
> > On Tue, Apr 28, 2020 at 09:30:06AM +0200, Michael Crusoe wrote:
> >> The guppy binary license is
> >> https://nanoporetech.com/sites/default/files/s3/terms/Nanopore-product-terms-and-conditions-nov2018-v2.pdf
> >> No source code is provided. No competitors of the company may use the
> >> software. Must be for "research use only".
> >>
> >> https://github.com/nanoporetech/flappie/blob/master/LICENCE.txt
> >> "Oxford Nanopore Technologies, Ltd. Public License Version 1.0" is used to
> >> license some of their "source available" software
> >> Only permits "research purposes", violating DFSG guideline #6 "No
> >> Discrimination Against Fields of Endeavor"
> >>
> >> https://github.com/haotianteng/Chiron/blob/master/LICENSE.md is the Mozilla
> >> Public License and is DFSG compatible
> >>
> >> On Mon, Apr 27, 2020 at 6:40 PM Ben Tris <[hidden email]> wrote:
> >>
> >>> Sorry to pop in.
> >>> I think this license should be reviewed,
> >>> unless sure it is not a free license.
> >>> To me it looks like a free software license.
> >>> Although not understand most.
> >>>
> >>> What is making this license non-free?
> >>>
> >>> On 27-04-20 17:06, Jun Aruga wrote:
> >>>> On Mon, Apr 27, 2020 at 4:43 PM Andreas Tille <[hidden email]> wrote:
> >>>>> Hi again,
> >>>>>
> >>>>> this brings up again my point: We *really*, *really* should take the
> >>>>> chance right now to ask upstreams for free licensing.  The time is good.
> >>>>> We just need somebody who is really doing this.
> >>>> For us, the free licensing is good. But for the company nanopore
> >>>> technologies it is their core competency.
> >>>> I am not sure we can make it happen, but it might be worth trying to ask.
> >>>>
> >>>>> On Mon, Apr 27, 2020 at 04:21:12PM +0200, Michael Crusoe wrote:
> >>>>>> Extracting the linked deb, one finds a binary and a very restrictive
> >>>>>> license. I do not believe that guppy source code is available nor it is
> >>>>>> likely to become available any time soon.
> >>>>>>
> >>>>>> While some of their other basecallers have source code available, I
> >>> would
> >>>>>> not call the license OSS:
> >>>>>> https://github.com/nanoporetech/flappie/blob/master/LICENCE.txt
> >>>> I found guppy client software that might be an alternative to use
> >>>> guppy's function.
> >>>> https://github.com/nanoporetech/pyguppyclient
> >>>>
> >>>> As Michael mentioned, checking other basecallers for nanopore, then
> >>>> communicating the nf-core/nanoseq project using the alternative base
> >>>> caller optionally.
> >>>>
> >>>> I found an interesting document about the basecallers.
> >>>> https://github.com/rrwick/Basecalling-comparison
> >>>>
> >>>> Performance of neural network basecalling tools for Oxford Nanopore
> >>> sequencing
> >>> https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1727-y
> >>>>> In this study, we tested four basecalling programs developed by ONT –
> >>> Albacore, Guppy, Scrappie and Flappie
> >>>>> ...
> >>>>> We also tested Chiron (https://github.com/haotianteng/Chiron), a
> >>> third-party basecaller still under development that uses a deeper neural
> >>> network than ONT’s basecallers [3].
> >>>> The third party basecaller Chiron's license is Mozilla Public License,
> >>> v. 2.0.
> >>>> https://github.com/haotianteng/Chiron/blob/master/LICENSE.md
> >>>>
> >>>
> >> --
> >> Michael R. Crusoe
>




--
http://fam-tille.de

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Re: Help for asking upstreams about free licenses urgently needed (Was: Help: Seeking source code of guppy base caller)

Ben Tris
I am willing to ask about guppy first, but what address could I use
best? And I'm afraid that I will not be that convincing, don't know the
exact use and needs for having guppy freed.

On 28-04-20 15:11, Andreas Tille wrote:

> Hi Ben,
>
> would you volunteer to contact the authors about this?
>
> Thanks a lot in advance
>
>       Andreas.
>
> On Tue, Apr 28, 2020 at 03:01:51PM +0200, Ben Tris wrote:
>> I was referring to the flappy license, that is mozilla like
>> maybe they are willing to change to MPL-2.0 that is GPL compatible
>> if that research only is a problem, but I think (guess) there are
>> enough escapes in the license.
>>
>> I still think there should be a confirmation
>> that guppy will not be available with a free software
>> license. Because I think it is developed with
>> contributions from the community.
>>
>> Otherwise it is indeed non-free.
>>
>> Based on the flappy license, should asked to release guppy with MPL-2.0?
>>
>> Someone mentioned chiron, maybe that is the only good alternative at
>> this moment?
>> (the Basecalling-comparison contains some additional advice on chiron
>> settings)
>>
>> On 28-04-20 10:11, Andreas Tille wrote:
>>> Hi Michael,
>>>
>>> thanks a lot for the links.  Any volunteer to start some discussion?
>>> As I said:  If we do not try nothing will change.  People with no
>>> technical skills could contribute by doing so to take some workload
>>> from packagers.
>>>
>>> I'll offer a $DRINK at next Debian Med sprint for every attempt to
>>> change a license. ;-)
>>>
>>> Kind regards
>>>
>>>       Andreas.
>>>
>>> On Tue, Apr 28, 2020 at 09:30:06AM +0200, Michael Crusoe wrote:
>>>> The guppy binary license is
>>>> https://nanoporetech.com/sites/default/files/s3/terms/Nanopore-product-terms-and-conditions-nov2018-v2.pdf
>>>> No source code is provided. No competitors of the company may use the
>>>> software. Must be for "research use only".
>>>>
>>>> https://github.com/nanoporetech/flappie/blob/master/LICENCE.txt
>>>> "Oxford Nanopore Technologies, Ltd. Public License Version 1.0" is used to
>>>> license some of their "source available" software
>>>> Only permits "research purposes", violating DFSG guideline #6 "No
>>>> Discrimination Against Fields of Endeavor"
>>>>
>>>> https://github.com/haotianteng/Chiron/blob/master/LICENSE.md is the Mozilla
>>>> Public License and is DFSG compatible
>>>>
>>>> On Mon, Apr 27, 2020 at 6:40 PM Ben Tris <[hidden email]> wrote:
>>>>
>>>>> Sorry to pop in.
>>>>> I think this license should be reviewed,
>>>>> unless sure it is not a free license.
>>>>> To me it looks like a free software license.
>>>>> Although not understand most.
>>>>>
>>>>> What is making this license non-free?
>>>>>
>>>>> On 27-04-20 17:06, Jun Aruga wrote:
>>>>>> On Mon, Apr 27, 2020 at 4:43 PM Andreas Tille <[hidden email]> wrote:
>>>>>>> Hi again,
>>>>>>>
>>>>>>> this brings up again my point: We *really*, *really* should take the
>>>>>>> chance right now to ask upstreams for free licensing.  The time is good.
>>>>>>> We just need somebody who is really doing this.
>>>>>> For us, the free licensing is good. But for the company nanopore
>>>>>> technologies it is their core competency.
>>>>>> I am not sure we can make it happen, but it might be worth trying to ask.
>>>>>>
>>>>>>> On Mon, Apr 27, 2020 at 04:21:12PM +0200, Michael Crusoe wrote:
>>>>>>>> Extracting the linked deb, one finds a binary and a very restrictive
>>>>>>>> license. I do not believe that guppy source code is available nor it is
>>>>>>>> likely to become available any time soon.
>>>>>>>>
>>>>>>>> While some of their other basecallers have source code available, I
>>>>> would
>>>>>>>> not call the license OSS:
>>>>>>>> https://github.com/nanoporetech/flappie/blob/master/LICENCE.txt
>>>>>> I found guppy client software that might be an alternative to use
>>>>>> guppy's function.
>>>>>> https://github.com/nanoporetech/pyguppyclient
>>>>>>
>>>>>> As Michael mentioned, checking other basecallers for nanopore, then
>>>>>> communicating the nf-core/nanoseq project using the alternative base
>>>>>> caller optionally.
>>>>>>
>>>>>> I found an interesting document about the basecallers.
>>>>>> https://github.com/rrwick/Basecalling-comparison
>>>>>>
>>>>>> Performance of neural network basecalling tools for Oxford Nanopore
>>>>> sequencing
>>>>> https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1727-y
>>>>>>> In this study, we tested four basecalling programs developed by ONT –
>>>>> Albacore, Guppy, Scrappie and Flappie
>>>>>>> ...
>>>>>>> We also tested Chiron (https://github.com/haotianteng/Chiron), a
>>>>> third-party basecaller still under development that uses a deeper neural
>>>>> network than ONT’s basecallers [3].
>>>>>> The third party basecaller Chiron's license is Mozilla Public License,
>>>>> v. 2.0.
>>>>>> https://github.com/haotianteng/Chiron/blob/master/LICENSE.md
>>>>>>
>>>> --
>>>> Michael R. Crusoe
>
>
>


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Re: Help for asking upstreams about free licenses urgently needed (Was: Help: Seeking source code of guppy base caller)

Andreas Tille-5
Hi Ben,

On Tue, Apr 28, 2020 at 03:16:56PM +0200, Ben Tris wrote:
> I am willing to ask about guppy first,

Thanks a lot.

> but what address could I use best?

May be you can check out the links Michael has given.  Does anybody
have some other points of contact?  I personally have no idea, sorry.

> And I'm afraid that I will not be that convincing, don't know the
> exact use and needs for having guppy freed.

I'd start with the fact that guppy is on our list of software that
is relevant to fight COVID-19.  At the end of our wiki page

   https://wiki.debian.org/DebianMed/SoftwareLiberation

is a nice link about kallisto featuring good arguments.

Hope this helps

      Andreas.
 

> On 28-04-20 15:11, Andreas Tille wrote:
> > Hi Ben,
> >
> > would you volunteer to contact the authors about this?
> >
> > Thanks a lot in advance
> >
> >       Andreas.
> >
> > On Tue, Apr 28, 2020 at 03:01:51PM +0200, Ben Tris wrote:
> >> I was referring to the flappy license, that is mozilla like
> >> maybe they are willing to change to MPL-2.0 that is GPL compatible
> >> if that research only is a problem, but I think (guess) there are
> >> enough escapes in the license.
> >>
> >> I still think there should be a confirmation
> >> that guppy will not be available with a free software
> >> license. Because I think it is developed with
> >> contributions from the community.
> >>
> >> Otherwise it is indeed non-free.
> >>
> >> Based on the flappy license, should asked to release guppy with MPL-2.0?
> >>
> >> Someone mentioned chiron, maybe that is the only good alternative at
> >> this moment?
> >> (the Basecalling-comparison contains some additional advice on chiron
> >> settings)
> >>
> >> On 28-04-20 10:11, Andreas Tille wrote:
> >>> Hi Michael,
> >>>
> >>> thanks a lot for the links.  Any volunteer to start some discussion?
> >>> As I said:  If we do not try nothing will change.  People with no
> >>> technical skills could contribute by doing so to take some workload
> >>> from packagers.
> >>>
> >>> I'll offer a $DRINK at next Debian Med sprint for every attempt to
> >>> change a license. ;-)
> >>>
> >>> Kind regards
> >>>
> >>>       Andreas.
> >>>
> >>> On Tue, Apr 28, 2020 at 09:30:06AM +0200, Michael Crusoe wrote:
> >>>> The guppy binary license is
> >>>> https://nanoporetech.com/sites/default/files/s3/terms/Nanopore-product-terms-and-conditions-nov2018-v2.pdf
> >>>> No source code is provided. No competitors of the company may use the
> >>>> software. Must be for "research use only".
> >>>>
> >>>> https://github.com/nanoporetech/flappie/blob/master/LICENCE.txt
> >>>> "Oxford Nanopore Technologies, Ltd. Public License Version 1.0" is used to
> >>>> license some of their "source available" software
> >>>> Only permits "research purposes", violating DFSG guideline #6 "No
> >>>> Discrimination Against Fields of Endeavor"
> >>>>
> >>>> https://github.com/haotianteng/Chiron/blob/master/LICENSE.md is the Mozilla
> >>>> Public License and is DFSG compatible
> >>>>
> >>>> On Mon, Apr 27, 2020 at 6:40 PM Ben Tris <[hidden email]> wrote:
> >>>>
> >>>>> Sorry to pop in.
> >>>>> I think this license should be reviewed,
> >>>>> unless sure it is not a free license.
> >>>>> To me it looks like a free software license.
> >>>>> Although not understand most.
> >>>>>
> >>>>> What is making this license non-free?
> >>>>>
> >>>>> On 27-04-20 17:06, Jun Aruga wrote:
> >>>>>> On Mon, Apr 27, 2020 at 4:43 PM Andreas Tille <[hidden email]> wrote:
> >>>>>>> Hi again,
> >>>>>>>
> >>>>>>> this brings up again my point: We *really*, *really* should take the
> >>>>>>> chance right now to ask upstreams for free licensing.  The time is good.
> >>>>>>> We just need somebody who is really doing this.
> >>>>>> For us, the free licensing is good. But for the company nanopore
> >>>>>> technologies it is their core competency.
> >>>>>> I am not sure we can make it happen, but it might be worth trying to ask.
> >>>>>>
> >>>>>>> On Mon, Apr 27, 2020 at 04:21:12PM +0200, Michael Crusoe wrote:
> >>>>>>>> Extracting the linked deb, one finds a binary and a very restrictive
> >>>>>>>> license. I do not believe that guppy source code is available nor it is
> >>>>>>>> likely to become available any time soon.
> >>>>>>>>
> >>>>>>>> While some of their other basecallers have source code available, I
> >>>>> would
> >>>>>>>> not call the license OSS:
> >>>>>>>> https://github.com/nanoporetech/flappie/blob/master/LICENCE.txt
> >>>>>> I found guppy client software that might be an alternative to use
> >>>>>> guppy's function.
> >>>>>> https://github.com/nanoporetech/pyguppyclient
> >>>>>>
> >>>>>> As Michael mentioned, checking other basecallers for nanopore, then
> >>>>>> communicating the nf-core/nanoseq project using the alternative base
> >>>>>> caller optionally.
> >>>>>>
> >>>>>> I found an interesting document about the basecallers.
> >>>>>> https://github.com/rrwick/Basecalling-comparison
> >>>>>>
> >>>>>> Performance of neural network basecalling tools for Oxford Nanopore
> >>>>> sequencing
> >>>>> https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1727-y
> >>>>>>> In this study, we tested four basecalling programs developed by ONT –
> >>>>> Albacore, Guppy, Scrappie and Flappie
> >>>>>>> ...
> >>>>>>> We also tested Chiron (https://github.com/haotianteng/Chiron), a
> >>>>> third-party basecaller still under development that uses a deeper neural
> >>>>> network than ONT’s basecallers [3].
> >>>>>> The third party basecaller Chiron's license is Mozilla Public License,
> >>>>> v. 2.0.
> >>>>>> https://github.com/haotianteng/Chiron/blob/master/LICENSE.md
> >>>>>>
> >>>> --
> >>>> Michael R. Crusoe
> >
> >
> >
>




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Re: Help for asking upstreams about free licenses urgently needed (Was: Help: Seeking source code of guppy base caller)

Jun Aruga-2
On Tue, Apr 28, 2020 at 4:31 PM Andreas Tille <[hidden email]> wrote:
>
> Hi Ben,
>
> On Tue, Apr 28, 2020 at 03:16:56PM +0200, Ben Tris wrote:
> > I am willing to ask about guppy first,
>
> Thanks a lot.

Thanks!

> > but what address could I use best?
>
> May be you can check out the links Michael has given.  Does anybody
> have some other points of contact?  I personally have no idea, sorry.
>
> > And I'm afraid that I will not be that convincing, don't know the
> > exact use and needs for having guppy freed.
>
> I'd start with the fact that guppy is on our list of software that
> is relevant to fight COVID-19.  At the end of our wiki page
>
>    https://wiki.debian.org/DebianMed/SoftwareLiberation

The information comes from the talk in nf-core Slack #covid19 channel.

Here is the link. If you join the Slack, maybe you can see it.

https://nfcore.slack.com/archives/C0105J0J9T8/p1587416769052300
> I can see nf-core/artic, nf-core/viralrecon, nf-core/nanoseq are used for that.
> ...
> The pipelines you listed are the ones that are/will be most applicable to COVID-19 analysis

nf-core/nanoseq project includes guppy as a dependency.

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Re: Help for asking upstreams about free licenses urgently needed (Was: Help: Seeking source code of guppy base caller)

Jun Aruga-2
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

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Re: Help for asking upstreams about free licenses urgently needed (Was: Help: Seeking source code of guppy base caller)

Andreas Tille-5
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.

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Re: Help for asking upstreams about free licenses urgently needed (Was: Help: Seeking source code of guppy base caller)

Charles Plessy-12
In reply to this post by Andreas Tille-2
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

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