Re: [MoM] Introduction

[Andreas Tille]

Dear Anne,

Am Mon, Mar 20, 2023 at 12:43:27PM + schrieb Anne Ghisla:
> I'm Anne Ghisla, working at Forschungzentrum Jülich as generalist /
> support tech, with close ties to NeuroDebian. I use Debian daily at
> work, used to be active in geospatial FOSS (OSGeo, Google Summer of
> Code), and now have the opportunity to dedicate time to Debian
> packaging.

Thank you for the introduction.  Also thanks for joining the video
conference yesterday - I wished more contributors would sneak in to
these short meetings since its nice to have some face to face
interaction.
 
> I wish to participate to the Mentoring of the Month project and for
> that I picked a tiny piece of software, written by our intern. I
> would like the mentoring month to be useful for us both, for me as
> packager, for him as upstream:
> https://github.com/psyinfra/prometheus_fzj_weather_exporter

Looks like a pretty good start regarding the personal need and
the (low) complexity of the software.  Since its not really a medical
package we should package this in Debian Science team (which is not
typical for the MoM projects but perfectly fine given your intention
to contribute to Debian Med with more complex packages later).  Thus
I've added you to the Debian Science team.
 
> Once I get familiar with tools and processes, my next goal is to address
> htcondor - most likely not alone, but Andreas mentioned yesterday
> during the videoconference that it requires some major (leg)work on
> copyright and I will be happy to pick that task.

That would be perfect!

> On the longer run, my plan is to take care of NeuroDebian packages.

This would be extremely welcome.

> I'm aware that I have quite a bit to catch up and I'm a bit intimidated,
> but I'm confident that through documentation and questions I will soon
> get familiar with the process, as all steps have defined actions :)

The goal of a MoM project is to wipe out all hurdles for newcomers.

> Thanks in advance for your support!
 
You are welcome

   Andreas.

-- 
http://fam-tille.de

[MoM] Introduction

[Anne Ghisla]

Hello all,

I'm Anne Ghisla, working at Forschungzentrum Jülich as generalist /
support tech, with close ties to NeuroDebian. I use Debian daily at
work, used to be active in geospatial FOSS (OSGeo, Google Summer of
Code), and now have the opportunity to dedicate time to Debian
packaging.

I wish to participate to the Mentoring of the Month project and for
that I picked a tiny piece of software, written by our intern. I
would like the mentoring month to be useful for us both, for me as
packager, for him as upstream:
https://github.com/psyinfra/prometheus_fzj_weather_exporter

Once I get familiar with tools and processes, my next goal is to address
htcondor - most likely not alone, but Andreas mentioned yesterday
during the videoconference that it requires some major (leg)work on
copyright and I will be happy to pick that task.
On the longer run, my plan is to take care of NeuroDebian packages.

I'm aware that I have quite a bit to catch up and I'm a bit intimidated,
but I'm confident that through documentation and questions I will soon
get familiar with the process, as all steps have defined actions :)

Thanks in advance for your support!
Kind regards,
Anne Ghisla (aghisla)



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Re: Self Introduction

[Nilesh Patra]

Please do not reply to me personally, rather reply on the list.
See below :-

On Fri, Apr 01, 2022 at 01:14:09AM +0530, Vinay wrote:
>> Cool. But I do not see this package in the archive.
>> Am I misunderstanding something? 
> The package isn't uploaded to the archive yet.

Okay, do you need sponsoring for this?
Where are your packaging changes, if you can link up?

> > Great, what tasks are you interested in doing?
> > If you are not sure, then for newcomer tasks you
> > could look into packages needing autopkgtest[1] pick a package
> > and add an autopkgtest to it.
> Sure will package and if any doubts can i drop the question on the
> matrix room or to the mailing list?

Mailing list is better for most queries, matrix is good for quick reports/quick 
queries.
Also, please head over to this link[2] and subscribe to the mailing list if you 
haven't already.

Let me know once you are done, so I/others will not have to CC you everytime and
you could read the replies from list mail.

> I would like to choose the package python-seqcluster , 

python-seqcluster is in contrib, and I am not sure if debci runs for contrib 
packages or not.
In any case, as first task, please do not work on seqcluster, rather 
choose a different package which is in main section instead.

> i'm new to
> autopkgtest any wiki links to refer to get started

Sure, you can take a look at the HOWTO here[3]
There are plenty of examples, you can for instance refer these[4-8]

Do not hesitate to ask if you need more help :)

> [1]: 
> https://salsa.debian.org/med-team/community/helper-scripts/-/blob/master/debian-med-tests.txt
[2]: https://lists.debian.org/debian-med/
[3]: 
https://salsa.debian.org/ci-team/autopkgtest/-/blob/master/doc/README.package-tests.rst
[4]: https://salsa.debian.org/med-team/shovill/-/tree/master/debian/tests
[5]: https://salsa.debian.org/med-team/bustools/-/tree/master/debian/tests
[6]: https://salsa.debian.org/med-team/busco/-/tree/master/debian/tests
[7]: https://salsa.debian.org/med-team/mafft/-/tree/master/debian/tests
[8]: https://salsa.debian.org/med-team/seqkit/-/tree/master/debian/tests

Regards,
Nilesh


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Re: Self Introduction

[Vinay]

On 01/04/22 00:41, Vinay wrote:


On 31/03/22 01:32, Nilesh Patra wrote:

On Thu, Mar 31, 2022 at 12:43:57AM +0530, Vinay wrote:

I am Vinay from India, a student currently pursuing Computer Science
Engineering.

Hello and welcome. I am from India as well so it is nice to
see you on this list.


I use GNU/Linux and have been using Debian for 2 years.
I have basic packaging skills, recently I started my journey in 
packaging a

node module (https://www.npmjs.com/package/prosemirror-view).

Cool. But I do not see this package in the archive.
Am I misunderstanding something?

The package isn't uploaded to the archive yet.
Furthermore, I have little knowledge about biology and medical 
applications,

and also would like to learn about it to get to started.
I would like to contribute to Debian.

Great, what tasks are you interested in doing?
If you are not sure, then for newcomer tasks you
could look into packages needing autopkgtest[1] pick a package
and add an autopkgtest to it.
Sure will package and if any doubts can i drop the question on the 
matrix room or to the mailing list?
[1]: 
https://salsa.debian.org/med-team/community/helper-scripts/-/blob/master/debian-med-tests.txt


I would like to choose the package python-seqcluster , i'm new to 
autopkgtest any wiki links to refer to get started




Regards,
Nilesh

Re: Self Introduction

[Vinay]

On 31/03/22 01:32, Nilesh Patra wrote:

On Thu, Mar 31, 2022 at 12:43:57AM +0530, Vinay wrote:

I am Vinay from India, a student currently pursuing Computer Science
Engineering.

Hello and welcome. I am from India as well so it is nice to
see you on this list.


I use GNU/Linux and have been using Debian for 2 years.
I have basic packaging skills, recently I started my journey in packaging a
node module (https://www.npmjs.com/package/prosemirror-view).

Cool. But I do not see this package in the archive.
Am I misunderstanding something?

The package isn't uploaded to the archive yet.

Furthermore, I have little knowledge about biology and medical applications,
and also would like to learn about it to get to started.
I would like to contribute to Debian.

Great, what tasks are you interested in doing?
If you are not sure, then for newcomer tasks you
could look into packages needing autopkgtest[1] pick a package
and add an autopkgtest to it.
Sure will package and if any doubts can i drop the question on the 
matrix room or to the mailing list?

[1]: 
https://salsa.debian.org/med-team/community/helper-scripts/-/blob/master/debian-med-tests.txt

Regards,
Nilesh

Re: Self Introduction

[Andreas Tille]

Hi,

Am Thu, Mar 31, 2022 at 01:32:31AM +0530 schrieb Nilesh Patra:
> On Thu, Mar 31, 2022 at 12:43:57AM +0530, Vinay wrote:
> > I am Vinay from India, a student currently pursuing Computer Science
> > Engineering.
> 
> Hello and welcome. I am from India as well so it is nice to
> see you on this list.

Welcome also from me from Europe. :-)

> > I use GNU/Linux and have been using Debian for 2 years.
> > I have basic packaging skills, recently I started my journey in packaging a
> > node module (https://www.npmjs.com/package/prosemirror-view).
> 
> Cool. But I do not see this package in the archive.
> Am I misunderstanding something?

I guess Nilesh means that there is no repository on salsa.debian.org.  I
guess you have a login there and you want to become a member of med-team
to contribute sensibly.
 
> > Furthermore, I have little knowledge about biology and medical applications,
> > and also would like to learn about it to get to started.
> > I would like to contribute to Debian.
> 
> Great, what tasks are you interested in doing? 
> If you are not sure, then for newcomer tasks you
> could look into packages needing autopkgtest[1] pick a package
> and add an autopkgtest to it.

The list Nilesh linked to[1] is ordering packages without autopkgtests
in the sequence of their usage number by popcon.  Please note that the
table contains a column which gives a hint about graphical user interface
where automated testing is probably quite hard (but might be possible
if the software contains some command line interface).

Kind regards

 Andreas.
 
> [1]: 
> https://salsa.debian.org/med-team/community/helper-scripts/-/blob/master/debian-med-tests.txt


-- 
http://fam-tille.de

Re: Self Introduction

[Nilesh Patra]

On Thu, Mar 31, 2022 at 12:43:57AM +0530, Vinay wrote:
> I am Vinay from India, a student currently pursuing Computer Science
> Engineering.

Hello and welcome. I am from India as well so it is nice to
see you on this list.

> I use GNU/Linux and have been using Debian for 2 years.
> I have basic packaging skills, recently I started my journey in packaging a
> node module (https://www.npmjs.com/package/prosemirror-view).

Cool. But I do not see this package in the archive.
Am I misunderstanding something?

> Furthermore, I have little knowledge about biology and medical applications,
> and also would like to learn about it to get to started.
> I would like to contribute to Debian.

Great, what tasks are you interested in doing? 
If you are not sure, then for newcomer tasks you
could look into packages needing autopkgtest[1] pick a package
and add an autopkgtest to it.

[1]: 
https://salsa.debian.org/med-team/community/helper-scripts/-/blob/master/debian-med-tests.txt

Regards,
Nilesh


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Self Introduction

[Vinay]

Hello
I am Vinay from India, a student currently pursuing Computer Science 
Engineering.

I use GNU/Linux and have been using Debian for 2 years.
I have basic packaging skills, recently I started my journey in 
packaging a node module (https://www.npmjs.com/package/prosemirror-view).
Furthermore, I have little knowledge about biology and medical 
applications, and also would like to learn about it to get to started.

I would like to contribute to Debian.


Kind Regards
        Vinay Keshava

---
    https://vinay-keshava.gitlab.io/

Re: Introduction

[Yaroslav Halchenko]

Hi Enric,

thank you for reaching out!  I just want to follow up on one aspect:
even without any coding/packaging, everyone can contribute to the big
long lasting positive effect for Debian and "Open"
science/software/health/... by promoting open practices, software and
licenses to apply and legal safeguards (e.g. participant consent forms
etc).  

Quite often in Debian (and elsewhere) we encounter interested in open
sharing researchers who have not thought about open sharing whenever
they initiated study or the project.  That often makes it hard or
impossible for THEM later to either share the products of their work, or
even at times to USE their own work (e.g. if they change
employers, or decide to reuse materials they have surrended their
copyright for).

Shameless plug: have a look at our very brief publication
https://academic.oup.com/gigascience/article/4/1/s13742-015-0072-7/2707572
principles of which apply also to improve reproducibility of research.
For that we promote thinking ahead while developing any
(neuroimaging in our case) study and provide this "short HOWTO" with
more pointers http://5steps.repronim.org/ .

So, altogether -- promoting healthy open practices from the beginning of
any study design/plan etc would be of great help to Debian and beyond.

Cheers,

On Sat, 02 Oct 2021, Enric Garcia Torrents wrote:

>Hello!

>I am Enric, new to the project. I am a medical anthropologist with very
>limited coding experience. My current research involves designing and
>developing an open source decision making support system, specifically for
>those cases regarded as severe by the current main psychiatric
>understanding. I hold the hope such system could be adapted for other
>uses, but that's the scope of what I am working on, fortunately with funds
>to carry on the work for five more years.

>My interest in Debian pure blends started ten years ago when I was
>fortunate to get involved in ArbyX, a Stanford Law School Codex' project
>on decision making in international arbitration courts. Unfortunately my
>involvement on that stalled for several reasons, but always kept in mind
>how important it is for people to have an access as easy as possible to
>free suits to do their job without worrying about very often unaffordable
>expenses, the burden of learning how to run the system at least as much as
>to install all packages and make them work without an issue, and so on.

>The arbitration project had a higher scope than the decision making one,
>but basically it's the same idea with a medical twist. That involved power
>maps of the players involved, and so do medicine. Involved adding data,
>and medicine -specially research and the development of treatments for new
>communities- also requires that. My experience, as I have been taught, is
>that software alone is not enough. Hopefully we can package it all, and
>create a tool set ready for those that need it.

>At the moment I really don't know how I can contribute other than maybe
>doing my best to help fire up other communities, help you spread the word
>about Debian Med, and help others join in the effort, on top of doing my
>very best to get to speed quickly on the Debian development part of it -as
>I mentioned to Andreas and the rest of the crew present on today's
>videocall (my apologies the connection was horrible and ran into other
>issues), I have next to zero idea on how to package and maintain-.

>No idea how long it take, because I am a medicine fresher too and that
>will take a massive amount of time. But I will, because I feel it's
>essential. Really admire what you have achieved developing Debian, it's
>impressive. Thanks.
-- 
Yaroslav O. Halchenko
Center for Open Neuroscience http://centerforopenneuroscience.org
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
WWW:   http://www.linkedin.com/in/yarik

Re: Introduction

[Andreas Tille]

Hi Enric,

Am Sat, Oct 02, 2021 at 08:41:16PM +0200 schrieb Enric Garcia Torrents:
> I am Enric, new to the project. I am a medical anthropologist with very
> limited coding experience. My current research involves designing and
> developing an open source decision making support system, specifically for
> those cases regarded as severe by the current main psychiatric
> understanding. I hold the hope such system could be adapted for other uses,
> but that's the scope of what I am working on, fortunately with funds to
> carry on the work for five more years.
> ...
> At the moment I really don't know how I can contribute other than maybe
> doing my best to help fire up other communities, help you spread the word
> about Debian Med, and help others join in the effort, on top of doing my
> very best to get to speed quickly on the Debian development part of it -as I
> mentioned to Andreas and the rest of the crew present on today's videocall
> (my apologies the connection was horrible and ran into other issues), I have
> next to zero idea on how to package and maintain-.

You are perfectly welcome here and what you consider tiny help is a
nice and welcome contribution.
 
Feel free to ask more questions here to get you up and running

Andreas.

-- 
http://fam-tille.de

Introduction

[Enric Garcia Torrents]

Hello!

I am Enric, new to the project. I am a medical anthropologist with very 
limited coding experience. My current research involves designing and 
developing an open source decision making support system, specifically 
for those cases regarded as severe by the current main psychiatric 
understanding. I hold the hope such system could be adapted for other 
uses, but that's the scope of what I am working on, fortunately with 
funds to carry on the work for five more years.


My interest in Debian pure blends started ten years ago when I was 
fortunate to get involved in ArbyX, a Stanford Law School Codex' project 
on decision making in international arbitration courts. Unfortunately my 
involvement on that stalled for several reasons, but always kept in mind 
how important it is for people to have an access as easy as possible to 
free suits to do their job without worrying about very often 
unaffordable expenses, the burden of learning how to run the system at 
least as much as to install all packages and make them work without an 
issue, and so on.


The arbitration project had a higher scope than the decision making one, 
but basically it's the same idea with a medical twist. That involved 
power maps of the players involved, and so do medicine. Involved adding 
data, and medicine -specially research and the development of treatments 
for new communities- also requires that. My experience, as I have been 
taught, is that software alone is not enough. Hopefully we can package 
it all, and create a tool set ready for those that need it.


At the moment I really don't know how I can contribute other than maybe 
doing my best to help fire up other communities, help you spread the 
word about Debian Med, and help others join in the effort, on top of 
doing my very best to get to speed quickly on the Debian development 
part of it -as I mentioned to Andreas and the rest of the crew present 
on today's videocall (my apologies the connection was horrible and ran 
into other issues), I have next to zero idea on how to package and 
maintain-.



No idea how long it take, because I am a medicine fresher too and that 
will take a massive amount of time. But I will, because I feel it's 
essential. Really admire what you have achieved developing Debian, it's 
impressive. Thanks.



--

Enric Garcia Torrents
Doctoral Researcher (MD-PhD trainee)
Medical Anthropology Research Center
Universitat Rovira i Virgili

https://enricgarcia.md 

Re: Introduction

[Étienne Mollier]

Hi Shruti,

Shruti Sridhar, on 2021-04-11 12:42:32 +0530:
> My name is Shruti Sridhar and I’m currently a senior at BITS Pilani Goa,
> India studying Biological Sciences and Chemical Engineering. I am reaching
> out in regards to the Debian Med project in this year’s Google Summer of
> Code for Quality Assurance and Continuous Integration for Bioinformatics
> Applications.
> 
> My major focus area (including my thesis topic during fall) is
> translational research. This area is extremely fast paced with new
> computational tools and workflows being introduced at a rapid speed. This
> is the reason the project with Debian Med resonates with me. It allows me
> to write relevant autopkgtests for a vast array of packages which is guided
> through the intersection of both my degrees and at the same time gives me
> exposure to the type of computational problems that exist and methods of
> approaching them.
> 
> I started contributing to Debian Med in August last year, and since then I
> have written tests for 8 packages. Lately, I have been working on the bugs
> filed as GSOC’21 applications tasks and have managed to close four of them.
> 
> I have shared a draft of my proposal through the GSoC portal, and I would
> kindly request the mentors to take a look and provide feedback so I can
> make any changes if required.

I'm afraid I'm not myself at ease with the gsoc administrivia.
However, I wanted to thank you for the test suites!  These are
not only useful for the package being tested per se, but also
when library dependencies are upgraded.  This allows us to
ascertain everything went well with the newer packages versions,
or to pinpoint breaking changes in newer libraries and inform
upstream of the evolution.  Last but not least, these packages
benefit from accelerated transition to Debian Testing during
normal development cycle, and can still migrate automatically
even during the current hard freeze, priod Debian stabilisation,
for the upcoming release.

It's really great to have someone from the field knowing how
these applications are bound together, and capable of producing
relevant test suite covering typical bioinformatics use cases!

> Looking forward to working with Debian Med!

Thanks again for your great work you already done!
Welcome on board!

Have a nice day,  :)
-- 
Étienne Mollier 
Fingerprint:  8f91 b227 c7d6 f2b1 948c  8236 793c f67e 8f0d 11da
Sent from /dev/pts/5, please excuse my verbosity.


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Introduction

[Shruti Sridhar]

Hello!

My name is Shruti Sridhar and I’m currently a senior at BITS Pilani Goa,
India studying Biological Sciences and Chemical Engineering. I am reaching
out in regards to the Debian Med project in this year’s Google Summer of
Code for Quality Assurance and Continuous Integration for Bioinformatics
Applications.

My major focus area (including my thesis topic during fall) is
translational research. This area is extremely fast paced with new
computational tools and workflows being introduced at a rapid speed. This
is the reason the project with Debian Med resonates with me. It allows me
to write relevant autopkgtests for a vast array of packages which is guided
through the intersection of both my degrees and at the same time gives me
exposure to the type of computational problems that exist and methods of
approaching them.

I started contributing to Debian Med in August last year, and since then I
have written tests for 8 packages. Lately, I have been working on the bugs
filed as GSOC’21 applications tasks and have managed to close four of them.

I have shared a draft of my proposal through the GSoC portal, and I would
kindly request the mentors to take a look and provide feedback so I can
make any changes if required.

Looking forward to working with Debian Med!

Regards,
Shruti

ᐧ

Re: Outreachy project: Provide introduction to microbiome analyses with Debian - inviting wet-lab researchers to Debian

[Andreas Tille]

Dear Tássia,

On Thu, Mar 11, 2021 at 07:49:16AM -0800, Tassia Camoes Araujo wrote:
> On 2021-03-07 18:47, Tassia Camoes Araujo wrote:
> > 
> > Please help shaping this proposal so it ***really*** makes sense and
> > attract interns ;-)
> > 
> Thanks to Steffen and Tony, the project is now on Outreachy's website
> waiting for approval from Debian coordinators.

Thanks a lot for pushing this

  Andreas. 

-- 
http://fam-tille.de

Outreachy project: Provide introduction to microbiome analyses with Debian - inviting wet-lab researchers to Debian

[Tassia Camoes Araujo]

Hi,

On 2021-03-07 18:47, Tassia Camoes Araujo wrote:
> 
> Please help shaping this proposal so it ***really*** makes sense and
> attract interns ;-)
> 
Thanks to Steffen and Tony, the project is now on Outreachy's website
waiting for approval from Debian coordinators.

Cheers,

Tassia. 

Re: "Introduction" tab on spreadsheet

[Steffen Möller]

On 07.12.20 13:46, Andrius Merkys wrote:
> Hello,
>
> On 2020-12-07 14:23, Steffen Möller wrote:
>> https://docs.google.com/spreadsheets/d/1tApLhVqxRZ2VOuMH_aPUgFENQJfbLlB_PFH_Ah_q7hM/edit#gid=1120557851
>>
>> I likely should spend less time on that nasty sheet and more on the
>> packaging. But I like it. And I keep having constructive 15 minutes
>> repeatedly that I use as a break to add/verify/update say bcbio links,
>> find packages not listed on our task pages, etc.
>>
>> No idea what this is evolving to. But I like it.
> Looks amazing!
>
> The introduction says "For write permissions to this spreadsheet please
> say hello on the Debian Med mailing list." I would like to add some
> details on one of the packages (qmean), could I?

YES!

Please just pm Jun (or me) an email that you allow google to see.

Steffen

Re: "Introduction" tab on spreadsheet

[Andrius Merkys]

Hello,

On 2020-12-07 14:23, Steffen Möller wrote:
> https://docs.google.com/spreadsheets/d/1tApLhVqxRZ2VOuMH_aPUgFENQJfbLlB_PFH_Ah_q7hM/edit#gid=1120557851
> 
> I likely should spend less time on that nasty sheet and more on the
> packaging. But I like it. And I keep having constructive 15 minutes
> repeatedly that I use as a break to add/verify/update say bcbio links,
> find packages not listed on our task pages, etc.
> 
> No idea what this is evolving to. But I like it.

Looks amazing!

The introduction says "For write permissions to this spreadsheet please
say hello on the Debian Med mailing list." I would like to add some
details on one of the packages (qmean), could I?

Best,
Andrius

"Introduction" tab on spreadsheet

[Steffen Möller]

https://docs.google.com/spreadsheets/d/1tApLhVqxRZ2VOuMH_aPUgFENQJfbLlB_PFH_Ah_q7hM/edit#gid=1120557851

I likely should spend less time on that nasty sheet and more on the
packaging. But I like it. And I keep having constructive 15 minutes
repeatedly that I use as a break to add/verify/update say bcbio links,
find packages not listed on our task pages, etc.

No idea what this is evolving to. But I like it.

Steffen

Re: [MoM] packaging gjh_asl_json (Was: Short Introduction)

[Andrei Rozanski]

Hi Andreas,

On 9/8/20 11:56 AM, Andreas Tille wrote:

Hi Andrei,

Not a problem at all. Thanks for answering.


sorry for the long delay which should remain untypical in a MoM project.
My weekend was occupied by real life and yesterday was a busy day.

On Fri, Sep 04, 2020 at 02:40:29PM +0200, Andrei Rozanski wrote:

I'll leave it to your preference since I don't mind much.  I guess it
makes those rows shorter whan just having names without links and thus
easier to edit - but as I said, I don't mind much.

gjh_asl_json asks for as part of the setup. Not sure if the "dependency"
should be a separate package...

So there is need to fetch |http://www.ampl.com/netlib/ampl/solvers.tgz - 
|https://salsa.debian.org/med-team/gjh-asl-json/-/blob/master/Thirdparty/get.ASL#L6

Ahhh, I was hoping that we will start with something simple but that's
for sure a new challenge.  Inside the packaging process you are not
allowed to download anything.  Code that is needed needs to be packaged
separately.  Usually you are lucky with this kind of scientific software
and so I tried to seek for it by

  apt-file search asl_pfg.h
  apt-file search avltree.h
  apt-file search jac2dim.h

Seeking this way in packages usually reveals in what package the header
files are available.  I'm mentioning this to explain what I'm using -
in the most cases successfully but it has no results so far.  However,
I've got something via

  apt-cache search netlib

shows that this is somehow related to the Basic Linear Algebra system
maintained in the Debian Science team.  I admit I'm not very well
educated about this.  To be sure I'd recommend to ask for advise there.


in order to be able to compile the program -
https://salsa.debian.org/med-team/gjh-asl-json/-/blob/master/Makefile#L27


Not sure if its fine to fetch it and ship with that in place. Or to have a
different package and add it as dependency.

Ok. I have asked them.

Yes, building a separate package netlib-ampl-solvers (or something like
this) might be necessary - but I'd advise to ask for more opinions on
Debian Science list.  This is also sensible in the MoM project to enable
you learning about those teams that might help you in your projects.


Thanks

Hope to be more responsive in the next couple of days.

Kind regards

   Andreas.


Thanks

Best,

AndreiR

Re: [MoM] packaging gjh_asl_json (Was: Short Introduction)

[Andreas Tille]

Hi Andrei,

sorry for the long delay which should remain untypical in a MoM project.
My weekend was occupied by real life and yesterday was a busy day.

On Fri, Sep 04, 2020 at 02:40:29PM +0200, Andrei Rozanski wrote:
> > I'll leave it to your preference since I don't mind much.  I guess it
> > makes those rows shorter whan just having names without links and thus
> > easier to edit - but as I said, I don't mind much.
> > > gjh_asl_json asks for as part of the setup. Not sure if the "dependency"
> > > should be a separate package...
> 
> So there is need to fetch |http://www.ampl.com/netlib/ampl/solvers.tgz - 
> |https://salsa.debian.org/med-team/gjh-asl-json/-/blob/master/Thirdparty/get.ASL#L6

Ahhh, I was hoping that we will start with something simple but that's
for sure a new challenge.  Inside the packaging process you are not
allowed to download anything.  Code that is needed needs to be packaged
separately.  Usually you are lucky with this kind of scientific software
and so I tried to seek for it by

 apt-file search asl_pfg.h
 apt-file search avltree.h
 apt-file search jac2dim.h

Seeking this way in packages usually reveals in what package the header
files are available.  I'm mentioning this to explain what I'm using -
in the most cases successfully but it has no results so far.  However,
I've got something via

 apt-cache search netlib

shows that this is somehow related to the Basic Linear Algebra system
maintained in the Debian Science team.  I admit I'm not very well
educated about this.  To be sure I'd recommend to ask for advise there.

> in order to be able to compile the program -
> https://salsa.debian.org/med-team/gjh-asl-json/-/blob/master/Makefile#L27
> 
> 
> Not sure if its fine to fetch it and ship with that in place. Or to have a
> different package and add it as dependency.

Yes, building a separate package netlib-ampl-solvers (or something like
this) might be necessary - but I'd advise to ask for more opinions on
Debian Science list.  This is also sensible in the MoM project to enable
you learning about those teams that might help you in your projects.

> Thanks

Hope to be more responsive in the next couple of days.

Kind regards

  Andreas.

-- 
http://fam-tille.de

Re: [MoM] packaging gjh_asl_json (Was: Short Introduction)

[Andrei Rozanski]

Hi Andreas,


On 9/4/20 1:12 PM, Andreas Tille wrote:

Hi Andrei

On Fri, Sep 04, 2020 at 11:50:44AM +0200, Andrei Rozanski wrote:

Thanks for the feedback. I see the point. Also with multiple selection was
not that big the effort ;)

Sure. :-)
  

I am happy to change the links if you provide one or I can get rid of them.

Fixed.

I'll leave it to your preference since I don't mind much.  I guess it
makes those rows shorter whan just having names without links and thus
easier to edit - but as I said, I don't mind much.
  

I am reading the https://www.debian.org/doc/manuals/maint-guide/ in order to
understand how to deal with the "ThirdParty" import that

gjh_asl_json asks for as part of the setup. Not sure if the "dependency"
should be a separate package...


So there is need to fetch |http://www.ampl.com/netlib/ampl/solvers.tgz - 
|https://salsa.debian.org/med-team/gjh-asl-json/-/blob/master/Thirdparty/get.ASL#L6 



in order to be able to compile the program - 
https://salsa.debian.org/med-team/gjh-asl-json/-/blob/master/Makefile#L27



Not sure if its fine to fetch it and ship with that in place. Or to have 
a different package and add it as dependency.




Please simply ask here what might be your exactproblem and do not hesitate
to push your reporitory soon.  May be we can give sensible hints more
quickly than if you read the whole maint-guide. ;-)
  
Kind regards


   Andreas.


Thanks

Best

AndreiR

Re: [MoM] packaging gjh_asl_json (Was: Short Introduction)

[Andreas Tille]

Hi Andrei

On Fri, Sep 04, 2020 at 11:50:44AM +0200, Andrei Rozanski wrote:
> Thanks for the feedback. I see the point. Also with multiple selection was
> not that big the effort ;)

Sure. :-)
 
> I am happy to change the links if you provide one or I can get rid of them.

I'll leave it to your preference since I don't mind much.  I guess it
makes those rows shorter whan just having names without links and thus
easier to edit - but as I said, I don't mind much.
 
> I am reading the https://www.debian.org/doc/manuals/maint-guide/ in order to
> understand how to deal with the "ThirdParty" import that
> 
> gjh_asl_json asks for as part of the setup. Not sure if the "dependency"
> should be a separate package...

Please simply ask here what might be your exactproblem and do not hesitate
to push your reporitory soon.  May be we can give sensible hints more
quickly than if you read the whole maint-guide. ;-)
 
Kind regards

  Andreas. 

-- 
http://fam-tille.de

Re: [MoM] packaging gjh_asl_json (Was: Short Introduction)

[Andrei Rozanski]

Hi Andreas,


Thanks for the feedback. I see the point. Also with multiple selection 
was not that big the effort ;)


I am happy to change the links if you provide one or I can get rid of them.


On 9/4/20 11:41 AM, Andreas Tille wrote:

On Thu, Sep 03, 2020 at 08:10:45PM +0200, Andrei Rozanski wrote:

Thanks! It worked.

Good.  I've seen you've spent a lot of time just to link my name to
wiki.d.o page.  While that's nice of you it would really not have been
worth that effort.  Its definitely not the best representation of my
work and not maintained at all. ;-)  But I agree that it now is closer
to the original page - thanks for it.


I am reading the https://www.debian.org/doc/manuals/maint-guide/ in 
order to understand how to deal with the "ThirdParty" import that


gjh_asl_json asks for as part of the setup. Not sure if the "dependency" 
should be a separate package...



Do you have any questions regarding your actual work on the gjh_asl_json
package?

Kind regards

   Andreas.



Thanks!

Best,

AndreiR

[MoM] packaging gjh_asl_json (Was: Short Introduction)

[Andreas Tille]

On Thu, Sep 03, 2020 at 08:10:45PM +0200, Andrei Rozanski wrote:
> Thanks! It worked.

Good.  I've seen you've spent a lot of time just to link my name to
wiki.d.o page.  While that's nice of you it would really not have been
worth that effort.  Its definitely not the best representation of my
work and not maintained at all. ;-)  But I agree that it now is closer
to the original page - thanks for it.

Do you have any questions regarding your actual work on the gjh_asl_json
package?

Kind regards

  Andreas.

-- 
http://fam-tille.de

Re: Short Introduction

[Andrei Rozanski]

Hi Andreas,


On 9/3/20 4:07 PM, Andreas Tille wrote:

Hi Andrei,

On Thu, Sep 03, 2020 at 02:49:41PM +0200, Andrei Rozanski wrote:

I have done only a few changes. Is it possible to give me permissions to
push the changes?


```

remote: You are not allowed to write to this project's wiki.

fatal: unable to access
'https://salsa.debian.org/med-team/community/MoM.wiki.git/': The requested
URL returned error: 403

```

Thanks! It worked.

I added rozanski to the Debian Med team which should be sufficient to
gain push permissions.

Thanks for your work on this

   Andreas.


Best,

AndreiR

Re: Short Introduction

[Andreas Tille]

Hi Andrei,

On Thu, Sep 03, 2020 at 02:49:41PM +0200, Andrei Rozanski wrote:
> 
> I have done only a few changes. Is it possible to give me permissions to
> push the changes?
> 
> 
> ```
> 
> remote: You are not allowed to write to this project's wiki.
> 
> fatal: unable to access
> 'https://salsa.debian.org/med-team/community/MoM.wiki.git/': The requested
> URL returned error: 403
> 
> ```

I added rozanski to the Debian Med team which should be sufficient to
gain push permissions.

Thanks for your work on this

  Andreas.

-- 
http://fam-tille.de

Re: Short Introduction

[Andrei Rozanski]

Hi Andreas,


On 9/3/20 8:18 AM, Andreas Tille wrote:

Hi Andrei,

On Wed, Sep 02, 2020 at 05:53:06PM +0200, Andrei Rozanski wrote:

Thanks for the help.

You are welcome.
  

I will check it.

Thanks.


Also, if needed, I could try to help migrating other pages.

Ok, thanks.

I do not think that anything will become structurally better if pages
will be migrated.  Admittedly our documentation is pretty poor but I do
not think this will change just because it will be placed at some other
Wiki (for sure I might be wrong here - its just my personal opinion).

The rationale behind moving the MoM page is that its just bad to move
newcomers into the situation in which you found yourself:  Make a lot of
effort to just add a single row to a table.  Since you need to create a
salsa.d.o login anyway if you want to join a MoM project I can now give
the advise:  "Please create a salsa login and add a row to the table on
the wiki page hosted in Salsa."  This makes way more sense than
confronting people with wiki.d.o.  BTW, there are good reasons to make
the creating-login-process so cumbersome since we were bothered by
spammers in the past.

Kind regards

 Andreas.



I have done only a few changes. Is it possible to give me permissions to 
push the changes?



```

remote: You are not allowed to write to this project's wiki.

fatal: unable to access 
'https://salsa.debian.org/med-team/community/MoM.wiki.git/': The 
requested URL returned error: 403


```


Thanks!

Best

AndreiR

Re: Short Introduction

[Andreas Tille]

Hi Andrei,

On Wed, Sep 02, 2020 at 05:53:06PM +0200, Andrei Rozanski wrote:
> Thanks for the help.

You are welcome.
 
> I will check it.

Thanks.

> Also, if needed, I could try to help migrating other pages.

I do not think that anything will become structurally better if pages
will be migrated.  Admittedly our documentation is pretty poor but I do
not think this will change just because it will be placed at some other
Wiki (for sure I might be wrong here - its just my personal opinion).

The rationale behind moving the MoM page is that its just bad to move
newcomers into the situation in which you found yourself:  Make a lot of
effort to just add a single row to a table.  Since you need to create a
salsa.d.o login anyway if you want to join a MoM project I can now give
the advise:  "Please create a salsa login and add a row to the table on
the wiki page hosted in Salsa."  This makes way more sense than
confronting people with wiki.d.o.  BTW, there are good reasons to make
the creating-login-process so cumbersome since we were bothered by
spammers in the past.

Kind regards

Andreas. 

-- 
http://fam-tille.de

Re: Short Introduction

[Andrei Rozanski]

Hi Andreas,

Thanks for the help.

On September 2, 2020 17:11:36 Andreas Tille  wrote:


Hi Andrei,

On Tue, Sep 01, 2020 at 09:49:42PM +0200, Andrei Rozanski wrote:

I am not bored about wikis but maybe I will accept your help since when
trying to create wiki account I get:


```

Account creation failed: Automatic account creation disabled to stop
spammers signing up. Please contact w...@debian.org and describe what you
want to do in the wiki. Please contact us in English, otherwise we will have
to pass your message to online translation services..

```


I will check it. Also, if needed, I could try to help migrating other pages.



I admit that's a real nuisance.  I'd like to stop this for ever now
and moved the whole Wiki page to

   https://salsa.debian.org/med-team/community/MoM/-/wikis/home

Since this has Markdown syntax and the old MoinMoin Wiki has some other
syntax it needed a bit of manual tweaking.  It would be really great
help if you could please proof read what I did and compare the old page

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

Please check whether my port was sensible and I have not forgot to
change some syntax somewhere as your first contribution.  Reading the
text again might help you anyway.

To do so simply create a Salsa account (which you need anyway) and add
yourself to the table.

Kind regards

 Andreas.

--
http://fam-tille.de



Best
AndreiR

Re: Short Introduction

[Andreas Tille]

Hi Andrei,

On Tue, Sep 01, 2020 at 09:49:42PM +0200, Andrei Rozanski wrote:
> I am not bored about wikis but maybe I will accept your help since when
> trying to create wiki account I get:
> 
> 
> ```
> 
> Account creation failed: Automatic account creation disabled to stop
> spammers signing up. Please contact w...@debian.org and describe what you
> want to do in the wiki. Please contact us in English, otherwise we will have
> to pass your message to online translation services..
> 
> ```

I admit that's a real nuisance.  I'd like to stop this for ever now
and moved the whole Wiki page to

https://salsa.debian.org/med-team/community/MoM/-/wikis/home

Since this has Markdown syntax and the old MoinMoin Wiki has some other
syntax it needed a bit of manual tweaking.  It would be really great
help if you could please proof read what I did and compare the old page

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

Please check whether my port was sensible and I have not forgot to
change some syntax somewhere as your first contribution.  Reading the
text again might help you anyway.

To do so simply create a Salsa account (which you need anyway) and add
yourself to the table.

Kind regards

  Andreas.

-- 
http://fam-tille.de

Re: Short Introduction

[Andrei Rozanski]

Hi Andreas,

I am not bored about wikis but maybe I will accept your help since when 
trying to create wiki account I get:



```

Account creation failed: Automatic account creation disabled to stop 
spammers signing up. Please contact w...@debian.org and describe what 
you want to do in the wiki. Please contact us in English, otherwise we 
will have to pass your message to online translation services..


```


On 9/1/20 9:13 PM, Andreas Tille wrote:

Hi Andrei,

you wrote in private mail that you are not sure what package to choose.
But MoM is always about open questions and answers.  ;-)  So I try to
clarify here.

On Tue, Sep 01, 2020 at 09:24:47AM +0200, Andrei Rozanski wrote:

Regarding machine learning we are in the process of packaging tensorflow
which requires some predependency.  On this front I lost track - but may
be someone can enlighten here.

On programming languages and environment, most of what I do involves bash 
scripting, GNU Make for pipelines, python and currently learning C++.

I think its a great idea. My vote is on the spreadsheet.

It would have been perfectly fine if you would have picked one.  I had
a very quick look into

 https://github.com/ghackebeil/gjh_asl_json

mentioned in the table.  I picked it since it is not even yet in Salsa
so you get the training of injecting it there.  From an extremely quick
look it seems to be sufficiently easy to package (we'll see whether I'm
correct here).


Also, will check MoM link.

Fine.  Just add a row in the Wiki table (or simply ask me to do so if
you are bored to create just another login on some "random" Wiki - there
is no strong need for you to create a login there).

You definitely need a login on Salsa (which makes me wonder whether I
should move the Wiki from wiki.debian.org to a Wiki on Salsa sooner or
later).


Many thanks!

You are welcome.  If there are any questions that are not really private
please simply post here and prefix the subject of your mail with [MoM].

Hope this helps

Andreas.



Thanks!

AndreiR

Re: Short Introduction

[Andrei Rozanski]

Hi Andreas,


Ok. Will do.

On 9/1/20 9:13 PM, Andreas Tille wrote:

Hi Andrei,

you wrote in private mail that you are not sure what package to choose.
But MoM is always about open questions and answers.  ;-)  So I try to
clarify here.

On Tue, Sep 01, 2020 at 09:24:47AM +0200, Andrei Rozanski wrote:

Regarding machine learning we are in the process of packaging tensorflow
which requires some predependency.  On this front I lost track - but may
be someone can enlighten here.

On programming languages and environment, most of what I do involves bash 
scripting, GNU Make for pipelines, python and currently learning C++.

I think its a great idea. My vote is on the spreadsheet.

Great, will look into it.

It would have been perfectly fine if you would have picked one.  I had
a very quick look into

 https://github.com/ghackebeil/gjh_asl_json

mentioned in the table.  I picked it since it is not even yet in Salsa
so you get the training of injecting it there.  From an extremely quick
look it seems to be sufficiently easy to package (we'll see whether I'm
correct here).


Also, will check MoM link.

Ok.

Fine.  Just add a row in the Wiki table (or simply ask me to do so if
you are bored to create just another login on some "random" Wiki - there
is no strong need for you to create a login there).

You definitely need a login on Salsa (which makes me wonder whether I
should move the Wiki from wiki.debian.org to a Wiki on Salsa sooner or
later).


Many thanks!

Got it.

You are welcome.  If there are any questions that are not really private
please simply post here and prefix the subject of your mail with [MoM].

Hope this helps

Andreas.


Thanks for clarifying.


Best

AndreiR

Re: Short Introduction

[Andreas Tille]

Hi Andrei,

you wrote in private mail that you are not sure what package to choose.
But MoM is always about open questions and answers.  ;-)  So I try to
clarify here.

On Tue, Sep 01, 2020 at 09:24:47AM +0200, Andrei Rozanski wrote:
> > Regarding machine learning we are in the process of packaging tensorflow
> > which requires some predependency.  On this front I lost track - but may
> > be someone can enlighten here.
> > > On programming languages and environment, most of what I do involves bash 
> > > scripting, GNU Make for pipelines, python and currently learning C++.
> I think its a great idea. My vote is on the spreadsheet.

It would have been perfectly fine if you would have picked one.  I had
a very quick look into

https://github.com/ghackebeil/gjh_asl_json

mentioned in the table.  I picked it since it is not even yet in Salsa
so you get the training of injecting it there.  From an extremely quick
look it seems to be sufficiently easy to package (we'll see whether I'm
correct here).

> Also, will check MoM link.

Fine.  Just add a row in the Wiki table (or simply ask me to do so if
you are bored to create just another login on some "random" Wiki - there
is no strong need for you to create a login there).

You definitely need a login on Salsa (which makes me wonder whether I
should move the Wiki from wiki.debian.org to a Wiki on Salsa sooner or
later).

> Many thanks!

You are welcome.  If there are any questions that are not really private
please simply post here and prefix the subject of your mail with [MoM]. 

Hope this helps

   Andreas.

-- 
http://fam-tille.de

Re: Short Introduction

[Andrei Rozanski]

Hi Andreas,


Thanks for the welcome!


On 8/31/20 11:08 PM, Andreas Tille wrote:

Hi Andrei,

thanks a lot for your interest in Debian Med (again - since I
also said so in private mail).

On Mon, Aug 31, 2020 at 09:15:43PM +0200, Andrei Rozanski wrote:

I am new to the project and I would like to introduce myself.

My name is Andrei Rozanski, currently I am a researcher in computational 
biology/bioinformatics at MPI-BPC.

I work with genomes and species comparison. Also, a little bit of machine 
learning and data analysis.

Regarding machine learning we are in the process of packaging tensorflow
which requires some predependency.  On this front I lost track - but may
be someone can enlighten here.
  

On programming languages and environment, most of what I do involves bash 
scripting, GNU Make for pipelines, python and currently learning C++.
I think its a great idea. My vote is on the spreadsheet. Also, will 
check MoM link.

In the COVID-19 hackathons we developed a spreadsheet

 
https://docs.google.com/spreadsheets/d/1tApLhVqxRZ2VOuMH_aPUgFENQJfbLlB_PFH_Ah_q7hM/edit?ts=5eb957ba#gid=543782716

which contains some todos and missings.  I would suggest we try to
package either some software you are using in your day to day work which
is not yet packaged for Debian or we pick from the spreadsheet above to
find a package where you can learn all things you need to know to work
smoothly and efficient inside the Debian Med team.  The formalisation
of this is done here

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

and this page contains a lot of links for newcomers you might like to
read.


Looking forward to contribute to the project!

Thanks a lot and looking forward to work together with you

 Andreas.



Many thanks!

AndreiR

Re: Short Introduction

[Andreas Tille]

Hi Andrei,

thanks a lot for your interest in Debian Med (again - since I
also said so in private mail).

On Mon, Aug 31, 2020 at 09:15:43PM +0200, Andrei Rozanski wrote:
> I am new to the project and I would like to introduce myself.
> 
> My name is Andrei Rozanski, currently I am a researcher in computational 
> biology/bioinformatics at MPI-BPC.
> 
> I work with genomes and species comparison. Also, a little bit of machine 
> learning and data analysis.

Regarding machine learning we are in the process of packaging tensorflow
which requires some predependency.  On this front I lost track - but may
be someone can enlighten here.
 
> On programming languages and environment, most of what I do involves bash 
> scripting, GNU Make for pipelines, python and currently learning C++.

In the COVID-19 hackathons we developed a spreadsheet


https://docs.google.com/spreadsheets/d/1tApLhVqxRZ2VOuMH_aPUgFENQJfbLlB_PFH_Ah_q7hM/edit?ts=5eb957ba#gid=543782716
 

which contains some todos and missings.  I would suggest we try to
package either some software you are using in your day to day work which
is not yet packaged for Debian or we pick from the spreadsheet above to
find a package where you can learn all things you need to know to work
smoothly and efficient inside the Debian Med team.  The formalisation
of this is done here

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

and this page contains a lot of links for newcomers you might like to
read.

> Looking forward to contribute to the project!

Thanks a lot and looking forward to work together with you

Andreas. 

-- 
http://fam-tille.de

Short Introduction

[Andrei Rozanski]

Hello all,


I am new to the project and I would like to introduce myself.

My name is Andrei Rozanski, currently I am a researcher in computational 
biology/bioinformatics at MPI-BPC.

I work with genomes and species comparison. Also, a little bit of machine 
learning and data analysis.

On programming languages and environment, most of what I do involves bash 
scripting, GNU Make for pipelines, python and currently learning C++.


Looking forward to contribute to the project!



Thanks!


Best Regards,

AndreiR

 

Re: Introduction: Jun Aruga

[Michael Crusoe]

On Mon, Mar 23, 2020 at 8:22 PM Jun Aruga  wrote:

> > > > I will be attending again, yes! I haven't decided on a particular
> proposal yet. Do you have any particular ideas?
> >
> > I'm currently waiting for getting the money back for my flight to
> > FOSSASIA in Singapore.  I intended to go there and by doing so consuming
> > my "Debian vacation" for this year.  Since "thanks" to Corona I might be
> > able to spent another week for Debian at some other event.  Its not
> > clear yet whether this will be DebConf or Biohackathon.
>
> Hi Andreas,
> It's great to meet you again!
>
> Okay. I have a willing to attend the Biohackathon this year in
> Barcelona, if the current COVID-19 issue will be fixed, and I can go
> outside Czech Republic.
>

If need be, the Europe Biohackathon will go virtual :-)

Applications are due April 2nd!

https://www.biohackathon-europe.org/proposalscall


-- 
Michael R. Crusoe

Re: Introduction: Jun Aruga

[Jun Aruga]

> > > I will be attending again, yes! I haven't decided on a particular 
> > > proposal yet. Do you have any particular ideas?
>
> I'm currently waiting for getting the money back for my flight to
> FOSSASIA in Singapore.  I intended to go there and by doing so consuming
> my "Debian vacation" for this year.  Since "thanks" to Corona I might be
> able to spent another week for Debian at some other event.  Its not
> clear yet whether this will be DebConf or Biohackathon.

Hi Andreas,
It's great to meet you again!

Okay. I have a willing to attend the Biohackathon this year in
Barcelona, if the current COVID-19 issue will be fixed, and I can go
outside Czech Republic.

> > Right now I have 2 ideas.
> > ...
> I like your ideas.
>
> No ideas from me to expect quickly, sorry.

Okay. I need to investigate or break down how my idea can be feasible.

Cheers,
Jun

-- 
Jun | He - His - Him

Re: Introduction: Jun Aruga

[Andreas Tille]

Hi Jun,

thank you for showing up here.

On Mon, Mar 16, 2020 at 04:13:06PM +0100, Jun Aruga wrote:
> > It was really nice to finally meet you and it was great to have you at the 
> > Sprint!
> 
> Hi Michael, it's great to meet you again.

+1
 
> > That's me and another well known Debian contributor in the video :-D 
> > https://www.youtube.com/watch?v=RNIInb72-z0
> 
> Yeah, I watched the video. I found that you and the well known Debian
> contributor :-D

:-P

> > I will be attending again, yes! I haven't decided on a particular proposal 
> > yet. Do you have any particular ideas?

I'm currently waiting for getting the money back for my flight to
FOSSASIA in Singapore.  I intended to go there and by doing so consuming
my "Debian vacation" for this year.  Since "thanks" to Corona I might be
able to spent another week for Debian at some other event.  Its not
clear yet whether this will be DebConf or Biohackathon.
 
> Right now I have 2 ideas.
> ...
I like your ideas.

No ideas from me to expect quickly, sorry.

Kind regards

  Andreas.

-- 
http://fam-tille.de

Re: Introduction: Jun Aruga

[Jun Aruga]

> Hey Jun!
>
> It was really nice to finally meet you and it was great to have you at the 
> Sprint!

Hi Michael, it's great to meet you again.

> That's me and another well known Debian contributor in the video :-D 
> https://www.youtube.com/watch?v=RNIInb72-z0

Yeah, I watched the video. I found that you and the well known Debian
contributor :-D

> I will be attending again, yes! I haven't decided on a particular proposal 
> yet. Do you have any particular ideas?

Right now I have 2 ideas.

First idea is to visualize DNA bases including non-coding DNA by the
type of segments such as Exon, Intron, SINE, LINE and etc. [1][2]
Because as a Software Engineer, it looks fun for me to understand the
DNA data statically rather than dynamically.
For the sequencing, it might be better to use yeasts' genome [3]
rather than human genome.
Because a human genome is 3 billions base pairs, a yeast is 12 million
base pairs. it seems that yeast is easier to analyze. I knew that the
yeast is used to predict human's non-coding DNA behavior.

Second idea is even more a stretch. That is hands on gene editing and
DNA sequencing for non-biologist.
I was inspired by the event that is held in Cambridge UK this month.
As far as I know, this event is Europe first event for gene editing
for non-biologists.
I have been talking with the event organizer from last month. And it
is planned that he will share with me about the recipe of the event at
the end of this month.
The detail is [4]. This event is funded by Mozilla Science organization. [5]
If gene editing has some difficulties, only sequencing by Oxford
Nanopore and store the data to the public database might be
interesting.

But I am not an expert. We need some help if we will do it.

Do you have ideas or opinions?


[1] 
https://en.wikipedia.org/wiki/Non-coding_DNA#Types_of_non-coding_DNA_sequences
[2] 
https://www.researchgate.net/figure/Distribution-of-rDNA-contacting-sites-in-different-portions-of-the-human-genome-A-and_fig3_337591505
[3] https://en.wikipedia.org/wiki/Yeast
[4] https://www.meetup.com/Cambridge-Synthetic-Biology-Meetup/events/268612875/
[5] 
https://biomake.space/home/blog/mozilla-grant-win-biomakespace-facilitates-accessible-gene-editing-and-dna-sequencing-technology

-- 
Jun | He - His - Him
jar...@redhat.com / IRC: jaruga

Re: Introduction: Jun Aruga

[Michael Crusoe]

On Sun, Mar 15, 2020 at 5:28 PM Jun Aruga  wrote:

> Hello Debian Med team,
>
> My name is Jun Aruga. I am a passionate hobbyist for the
> bioinformatics. Especially genome sequencing area.
>
> I had an opportunity to join Debian Med Sprint event last month in Berlin.
> it was very fun, and inspired me.
>
> https://wiki.debian.org/Sprints/2020/Debian%20Med%20Sprint%20Feb%202020%2C%20Berlin


Hey Jun!

It was really nice to finally meet you and it was great to have you at the
Sprint!


>
>
> As I am usually at Fedora project, and maybe I can not work directly
> for the Debian packaging.
> But I am happy to contribute something to bio open source projects,
> when Debian Med team needs it.
>
> I am looking forward to seeing you, and work together again.
>
>
> P.S. I noticed that this year's Biohackathon Europe event is on the
> website now.
>
> https://www.biohackathon-europe.org/
> > BARCELONA 2020 NOVEMBER 9th - 13th
> > Call to proposals now open
>
> Are you planning to do something for the event?
> I love I am involved.
>

That's me and another well known Debian contributor in the video :-D
https://www.youtube.com/watch?v=RNIInb72-z0

I will be attending again, yes! I haven't decided on a particular proposal
yet. Do you have any particular ideas?


>
> Cheers,
> Jun
>
> --
> Jun | He - His - Him
> jar...@redhat.com / IRC: jaruga
>
>

-- 
Michael R. Crusoe

Introduction: Jun Aruga

[Jun Aruga]

Hello Debian Med team,

My name is Jun Aruga. I am a passionate hobbyist for the
bioinformatics. Especially genome sequencing area.

I had an opportunity to join Debian Med Sprint event last month in Berlin.
it was very fun, and inspired me.
https://wiki.debian.org/Sprints/2020/Debian%20Med%20Sprint%20Feb%202020%2C%20Berlin

As I am usually at Fedora project, and maybe I can not work directly
for the Debian packaging.
But I am happy to contribute something to bio open source projects,
when Debian Med team needs it.

I am looking forward to seeing you, and work together again.


P.S. I noticed that this year's Biohackathon Europe event is on the website now.

https://www.biohackathon-europe.org/
> BARCELONA 2020 NOVEMBER 9th - 13th
> Call to proposals now open

Are you planning to do something for the event?
I love I am involved.

Cheers,
Jun

-- 
Jun | He - His - Him
jar...@redhat.com / IRC: jaruga

Re: Introduction post- OUTREACHY APPLICANT

[Andreas Tille]

Hi Anandi,

On Mon, Mar 09, 2020 at 08:22:26PM +0530, Anandi Puritipati wrote:
> My name is Anandi and I'm an applicant of the Outreachy May 2020 Internship
> round! I am a masters graduate in the field of Biological Engineering from
> the Indian Institute of Technology, Madras and I am really interested in
> contributing to Debian as part of my initial application!
> I'm fairly well versed in Python and I am very excited to be able to learn
> and grow as I work. I would be really grateful if you guys could help me
> out with this round by letting me know how I can contribute to your team!

The mailing list archive of the Debian Med mailing list contains some
hints how to start.  I'd recommend the mailing list archives from last
February[1] or March[2] featuring the term "test" in subject.  I'd
specifically recommend my mail[3] about the automatic generation of a
task list.

If you can not obtain a task from these hints that's perfectly fine.  We
are happy to give more detailed hints once we might know more about your
skills to let us know what exact information might be helpful for you.

> Thank you so much for this opportunity!

You are welcome.

Kind regards and thanks for your interest in our outreachy project

 Andreas.

[1] https://lists.debian.org/debian-med/2020/02/threads.html
[2] https://lists.debian.org/debian-med/2020/03/threads.html
[3] https://lists.debian.org/debian-med/2020/02/msg00096.html

-- 
http://fam-tille.de

Introduction post- OUTREACHY APPLICANT

[Anandi Puritipati]

Hi!

My name is Anandi and I'm an applicant of the Outreachy May 2020 Internship
round! I am a masters graduate in the field of Biological Engineering from
the Indian Institute of Technology, Madras and I am really interested in
contributing to Debian as part of my initial application!
I'm fairly well versed in Python and I am very excited to be able to learn
and grow as I work. I would be really grateful if you guys could help me
out with this round by letting me know how I can contribute to your team!

Thank you so much for this opportunity!

Best Regards,
Anandi Puritipati.

Re: w1bw introduction

[Steffen Möller]

Hello,

On 23.02.19 21:05, Andreas Tille wrote:

Hi Bruce,

On Sat, Feb 23, 2019 at 10:04:18AM -0500, Bruce Walker wrote:

Debin-Med team,

I wanted to introduce myself with the intent of helping out.

I was a DD back in the 2000s (retired emeritus), and I'm interested in
becoming active again. I've also done quite a bit of scientific computing
in general and computational biology in particular, especially genome
assembly, assembly improvement, and variant calling software (e.g., Pilon
is a tool I wrote and published about 5 years ago and still maintain, and
it looks as if this group recently packaged it).

I propose you find some biological theme that is of your interest and
we see that we get the tools together to establish a reasonable
Open Source workflow towards it. We have a few genome assemblers from
a few years ago but I admit not to know where the state of the art is as 
of today.


Welcome!

Steffen

Re: w1bw introduction

[Andreas Tille]

Hi Bruce,

On Sat, Feb 23, 2019 at 10:04:18AM -0500, Bruce Walker wrote:
> Debin-Med team,
> 
> I wanted to introduce myself with the intent of helping out.
> 
> I was a DD back in the 2000s (retired emeritus), and I'm interested in
> becoming active again. I've also done quite a bit of scientific computing
> in general and computational biology in particular, especially genome
> assembly, assembly improvement, and variant calling software (e.g., Pilon
> is a tool I wrote and published about 5 years ago and still maintain, and
> it looks as if this group recently packaged it).

Yes, we did.  Do you want to add yourself as Uploader for this package?
 
> For the moment, I am monitoring the list and re-familiarizing myself with
> DD processes. If there's anything urgent, I can try to jump in, meanwhile
> I'll be getting up to speed.

I think we are in a quite good shape.  Regarding pilon itself I had some
trouble with Pilon in the first place since Scala is in a bad shape
inside Debian (there is a recent discussion on debian-java list).  May
be if you have some background with Scala and Java and can help there.
We have definitely some need of people with some skills in Java and some
open packaging tasks.  It would be great if you could join that effort.
To get started in the team it would be good to register on
salsa.debian.org and apply for Debian Med team membership.

> --bruce (formerly w...@debian.org)

As far as I know becoming an active DD from emeritus status should not
be that hard.

Thanks a lot for your interest and welcome in the team

 Andreas.

-- 
http://fam-tille.de

w1bw introduction

[Bruce Walker]

Debin-Med team,

I wanted to introduce myself with the intent of helping out.

I was a DD back in the 2000s (retired emeritus), and I'm interested in
becoming active again. I've also done quite a bit of scientific computing
in general and computational biology in particular, especially genome
assembly, assembly improvement, and variant calling software (e.g., Pilon
is a tool I wrote and published about 5 years ago and still maintain, and
it looks as if this group recently packaged it).

For the moment, I am monitoring the list and re-familiarizing myself with
DD processes. If there's anything urgent, I can try to jump in, meanwhile
I'll be getting up to speed.

--bruce (formerly w...@debian.org)

Re: introduction and outreachy

[Steffen Möller]

Hi Joannis,

On 18.10.18 03:36, Ioannis Valasakis wrote:
I am Ioannis and I want to be part of Outreachy this year :) I am 
completing my MSc in Bionformatics so I find this is a very suitable 
place for me. I also love Debian and using it since mny years, so 
I am very excited to submit a proposal!


I admit to only now have read up about what Outreachy exactly is. Good 
luck for your proposal. Tell me/the list how I/we can help.


Since you are completing your degree in the field, my personal advice 
would be to take this funded time (or any self-funded time which your 
thesis work would likely be) to prepare for what you want to do 
afterwards. You may decide to look for some piece of biology that is of 
your interest, look for software supporting that (OMICtools.com and 
bio.tools may help here) and see what part of it is already represented 
on Debian Med. The delta of it may define your project.


Synthetic biology and more recently also Immunoinformatics is what I 
personally like to see addressed more. That said, we still have issues 
to get some current basic workflows like 
https://github.com/bcbio/bcbio-nextgen or 
https://software.broadinstitute.org/gatk/ smoothly integrated with us. 
This is especially important also for continuous integration testing all 
the libraries and tools underneath. Also, the pipelines still emerging 
for the Nanopore are not fully with us, yet. This has a bit of a 
"homework to do" kind of character.


Best,

Steffen

Re: introduction and outreachy

[Andreas Tille]

Hi Ioannis,

On Thu, Oct 18, 2018 at 02:36:04AM +0100, Ioannis Valasakis wrote:
> Hi all! I am Ioannis and I want to be part of Outreachy this year :) I am 
> completing my MSc in Bionformatics so I find this is a very suitable place 
> for me. I also love Debian and using it since mny years, so I am very 
> excited to submit a proposal! Regards Ioannis

Welcome to Debian Med Outreachy.  Please come up here with any questions
you might have.

Kind regards

   Andreas.

-- 
http://fam-tille.de

introduction and outreachy

[Ioannis Valasakis]

Hi all! I am Ioannis and I want to be part of Outreachy this year :) I am 
completing my MSc in Bionformatics so I find this is a very suitable place for 
me. I also love Debian and using it since mny years, so I am very excited 
to submit a proposal! Regards Ioannis

Re: Introduction

[Manas Kashyap]

Hola Mentor,
I applied for outreachy yesterday and i got a mail stating my initial
application is rejected , so is there a way still to be in outreachy ? like
being a co-mentor or something ??

On Wed, Oct 3, 2018 at 3:12 AM Andreas Tille  wrote:

> Hi Manas,
>
> On Tue, Oct 02, 2018 at 10:17:30PM +0530, Manas Kashyap wrote:
> > Hahaha no nothing like that. I am just a beginner and looking forward to
> > learn things.
>
> OK.  That's a very sensible way to learn.
>
> > Well the thing is if can anyone connect me to riot channel or Irc
> channel i
> > can msg their my problems i am facing for adding autopkgtest for med team
> > repos
>
> Sorry, I'm not (yet) on any riot channel.  I'm also rarely on
> #debian-med IRC (but may be you simply try).  I'm fine with IRC
> appointments but not this week.  Otherwise I hope the information
> I gave in my last mail about autopkgtests were helpful - if not
> may be you ask via e-mail on the list.
>
> Kind regards
>
> Andreas.
>
> > On Tue 2 Oct, 2018, 6:42 PM Andreas Tille,  wrote:
> >
> > > Hi Manas,
> > >
> > > On Tue, Oct 02, 2018 at 01:02:43PM +0530, Manas Kashyap wrote:
> > > > Hola Guys ,
> > > > I am Manas Kashyap currently an undergrad from India .
> > > > I have been in packaging for past 1 year and have packaged many node
> ,
> > > ruby
> > > > and go modules and maintained modules of python , go , ruby , node ,
> > > fonts
> > > > too . I have also worked with many open source projects like
> > > hamaralinux.org
> > > > , worked with docker and instances and would love to learn from you
> all
> > > as
> > > > i am just a beginner.
> > >
> > > Sounds like "advanced beginner" is the proper description. ;-)
> > >
> > > > I am part of debian ruby , js , go , fonts team and currently i have
> > > worked
> > > > on gitlab packaging .
> > > > Now , i would like to work on debian Med projects too and help them
> in
> > > > maintaining them .
> > >
> > > That's very good news since we can definitely profit from more help.
> > >
> > > Just let us know here if you need hints to kick-start your work on
> > > Debian Med packages.
> > >
> > > > Thank you
> > > > Manas Kashyap
> > >
> > > Thanks a lot to you
> > >
> > >  Andreas.
> > >
> > > > http://wiki.debian.org/ManasKashyap
> > >
> > > --
> > > http://fam-tille.de
> > >
> > >
>
> --
> http://fam-tille.de
>

Re: Introduction

[Andreas Tille]

Hi Manas,

On Tue, Oct 02, 2018 at 10:17:30PM +0530, Manas Kashyap wrote:
> Hahaha no nothing like that. I am just a beginner and looking forward to
> learn things.

OK.  That's a very sensible way to learn.

> Well the thing is if can anyone connect me to riot channel or Irc channel i
> can msg their my problems i am facing for adding autopkgtest for med team
> repos

Sorry, I'm not (yet) on any riot channel.  I'm also rarely on
#debian-med IRC (but may be you simply try).  I'm fine with IRC
appointments but not this week.  Otherwise I hope the information
I gave in my last mail about autopkgtests were helpful - if not
may be you ask via e-mail on the list.

Kind regards

Andreas.

> On Tue 2 Oct, 2018, 6:42 PM Andreas Tille,  wrote:
> 
> > Hi Manas,
> >
> > On Tue, Oct 02, 2018 at 01:02:43PM +0530, Manas Kashyap wrote:
> > > Hola Guys ,
> > > I am Manas Kashyap currently an undergrad from India .
> > > I have been in packaging for past 1 year and have packaged many node ,
> > ruby
> > > and go modules and maintained modules of python , go , ruby , node ,
> > fonts
> > > too . I have also worked with many open source projects like
> > hamaralinux.org
> > > , worked with docker and instances and would love to learn from you all
> > as
> > > i am just a beginner.
> >
> > Sounds like "advanced beginner" is the proper description. ;-)
> >
> > > I am part of debian ruby , js , go , fonts team and currently i have
> > worked
> > > on gitlab packaging .
> > > Now , i would like to work on debian Med projects too and help them in
> > > maintaining them .
> >
> > That's very good news since we can definitely profit from more help.
> >
> > Just let us know here if you need hints to kick-start your work on
> > Debian Med packages.
> >
> > > Thank you
> > > Manas Kashyap
> >
> > Thanks a lot to you
> >
> >  Andreas.
> >
> > > http://wiki.debian.org/ManasKashyap
> >
> > --
> > http://fam-tille.de
> >
> >

-- 
http://fam-tille.de

Re: Introduction

[Manas Kashyap]

Hahaha no nothing like that. I am just a beginner and looking forward to
learn things.
Well the thing is if can anyone connect me to riot channel or Irc channel i
can msg their my problems i am facing for adding autopkgtest for med team
repos

On Tue 2 Oct, 2018, 6:42 PM Andreas Tille,  wrote:

> Hi Manas,
>
> On Tue, Oct 02, 2018 at 01:02:43PM +0530, Manas Kashyap wrote:
> > Hola Guys ,
> > I am Manas Kashyap currently an undergrad from India .
> > I have been in packaging for past 1 year and have packaged many node ,
> ruby
> > and go modules and maintained modules of python , go , ruby , node ,
> fonts
> > too . I have also worked with many open source projects like
> hamaralinux.org
> > , worked with docker and instances and would love to learn from you all
> as
> > i am just a beginner.
>
> Sounds like "advanced beginner" is the proper description. ;-)
>
> > I am part of debian ruby , js , go , fonts team and currently i have
> worked
> > on gitlab packaging .
> > Now , i would like to work on debian Med projects too and help them in
> > maintaining them .
>
> That's very good news since we can definitely profit from more help.
>
> Just let us know here if you need hints to kick-start your work on
> Debian Med packages.
>
> > Thank you
> > Manas Kashyap
>
> Thanks a lot to you
>
>  Andreas.
>
> > http://wiki.debian.org/ManasKashyap
>
> --
> http://fam-tille.de
>
>

Re: Introduction

[Andreas Tille]

Hi Manas,

On Tue, Oct 02, 2018 at 01:02:43PM +0530, Manas Kashyap wrote:
> Hola Guys ,
> I am Manas Kashyap currently an undergrad from India .
> I have been in packaging for past 1 year and have packaged many node , ruby
> and go modules and maintained modules of python , go , ruby , node , fonts
> too . I have also worked with many open source projects like hamaralinux.org
> , worked with docker and instances and would love to learn from you all as
> i am just a beginner.

Sounds like "advanced beginner" is the proper description. ;-)

> I am part of debian ruby , js , go , fonts team and currently i have worked
> on gitlab packaging .
> Now , i would like to work on debian Med projects too and help them in
> maintaining them .

That's very good news since we can definitely profit from more help.

Just let us know here if you need hints to kick-start your work on
Debian Med packages.

> Thank you
> Manas Kashyap

Thanks a lot to you

 Andreas.

> http://wiki.debian.org/ManasKashyap

-- 
http://fam-tille.de

Introduction

[Manas Kashyap]

Hola Guys ,
I am Manas Kashyap currently an undergrad from India .
I have been in packaging for past 1 year and have packaged many node , ruby
and go modules and maintained modules of python , go , ruby , node , fonts
too . I have also worked with many open source projects like hamaralinux.org
, worked with docker and instances and would love to learn from you all as
i am just a beginner.
I am part of debian ruby , js , go , fonts team and currently i have worked
on gitlab packaging .
Now , i would like to work on debian Med projects too and help them in
maintaining them .
Thank you
Manas Kashyap
http://wiki.debian.org/ManasKashyap

Re: Introduction

[Andreas Tille]

Hi Redmar,

thanks for you interest in Debian Med.

On Sun, May 14, 2017 at 01:56:30PM +0200, Redmar wrote:
> My name is Redmar, and I work as a bioinformatician in food safety. I
> would like to contribute to Debian Med by packaging applications. This
> is something I already do for my job, and I would like to improve my
> packages and share them with the community. 

That's pretty cool.  I wished we would have every week ... OK month a
mail like this and I think you did the perfectly correct step to contact
us.
 
> I have looked at https://www.debian.org/devel/debian-med/ but there is
> a lot of information there. What is the best place to start reading?

Considering you have some packaging skills the most straigthforward
document which makes you up and running is the Debian Med team policy
document[1].
 
> Recently I created a working package for LisSero using equivs-build,
> what would be the next step to make this package available for regular
> users?
> 
> https://github.com/Redmar-van-den-Berg/LisSero/blob/master/debian

Hmmm, equivs-build is definitely not what we want to use for official
packaging but its nice that you found a starting point.  I'd suggest you
might join a so called Mentoring of the Month project[2] and we bring
LisSero into a Debian releasable shape.  What do you think about this?
While there is currently a MoM student for May I have the feeling that
LisSero might be a project that is bearable in addition and I consider
it very important that you would learn the correct way to bring
packages into Debian if packaging belongs to your daily work anyway.

BTW, I've noticed that IsPcr is an optional part of LisSero.  There is a
long standing discussion about the licensing of Jim Kents software and
that we need some final clarification about this.  Its similar with
seqsero which I recently packaged for Debian[3] and I think it might be
a very educational lesson for you to learn discussing with upstream
about licenses.

Thanks for raising your voice here and I'm happy to help you starting
with official Debian packaging.  Kind regards

  Andreas.

[1] https://debian-med.alioth.debian.org/docs/policy.html
[2] https://wiki.debian.org/DebianMed/MoM
[3] https://blends.debian.org/med/tasks/bio#seqsero

-- 
http://fam-tille.de

Re: Introduction

[Andreas Tille]

Hi David,

On Fri, Jun 21, 2013 at 03:28:45PM +0200, David Parsons wrote:
 Hi again,
 
 I've just commited the changes, pdebuild looks OK, although it does
 complain about some hooks not being found.

I'm not sure what hooks you might mean - my pbuilder run was perfectly
fine.  I fixed a lintian error (you should not Build-Depends on
Build-Essential packages (libc6-dev) by just removing libc6-dev and some
minor spelling, formatting things mentioned by lintian.

 I'll be away for two weeks so don't take it personally if I don't
 answer ;-)

If it's vacation just enjoy it.  We need to wait with the upload until
the source of the pdf documentation is provided.  I also would be happy
if we could sort out the issue that the internal utilities end up in
/usr/bin instead of /usr/lib/kissplice - what do you think about my
suggestion?

If anybody else might be interested in this package as well - you've got
two weeks to provide a patch. ;-)

Kind regards

   Andreas.
 
 Le 21/06/2013 11:41, Andreas Tille a écrit :
 Hi David,
 
 On Fri, Jun 21, 2013 at 10:37:50AM +0200, David Parsons wrote:
 I didn't write manpages for the other executables because they
 shouldn't be called directly from the user. The main executable is
 actually a python script that calls all the other executables in an
 integrated pipeline (with some executions being done in parallel) .
 I personally don't like the multi-binary arch very much but I won't
 be able to modify this right now. I'll talk about that with the
 upstream team.
 The best way to fix this would be to move the binaries in question
 to /usr/lib/kissplice and adapt the PATH inside the main program.
 Given the fact that it is somehow about esthetics I would not call
 this a stumbling stone for a first upload, but it would be nice to
 have a better design.
 
 Finally the source would be considered as non-free because the source
 for doc/user_guide.pdf is missing.  The best way to fix this is to ask
 upstream for the LaTeX source of this documentation.  If they do not
 want to distribute this source we need to remove the doc from the source
 tarball (which would be suboptimal, thought).  Given that upstream is
 cooperative the doc should also be installed into the binary package -
 just mention it in debian/docs.
 I'll add the .tex and add it to the binary package
 It only needs to be inside the *source* package.  It is sufficient to
 ship (even the prebuilded) PDF inside the binary, but the source simply
 needs to exist.
 
 Thanks a lot !
 You are welcome
 
 Andreas.
 
 
 
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 To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org
 with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
 Archive: http://lists.debian.org/51c4550d.2010...@inria.fr
 
 

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Re: Introduction

[David Parsons]

Hi Andreas,


Le 18/06/2013 10:38, Andreas Tille a écrit :

Hi David,

On Mon, Jun 17, 2013 at 11:59:26PM +0200, Andreas Tille wrote:

I suppose I've misunderstood something. Am I not supposed to add
the package to the “task”file where it fits the best ?

Don't worry - I can easily add it.  You are no member of the Blends team
which is no real harm if you just want to add this single package - I'll
do it tomorrow.

Done to bio and bio-ngs.  Remark:  Bio-ngs is currently a subset of bio
which is only rendered at the web pages but not turned into a
metapackage.  This is somehow questionable but we did not yet found a
reasonable solution how to reasonably split up the whole set of
biological packages.  I personally feel unable to do this in a
reasonable manner because I'm no biologist (I'm physicist by profession)
and so far nobody took over the work to find a reasonable split.  The
bio-ngs and bio-phylogeny tasks are some first try to experiment with
some more fine grained tasks but if we miss to inject a package into
(main) bio it will not create a metapackage dependency.  Feel free to
make some suggestions how we could enhance this situation.


I won't be of a great help for splitting the set of biological packages 
since I'm not a biologist either.
I had a question regarding the metapackages (MP for short) however. Can 
a MP be included in another MP ? If so bio-ngs could be a dependency of 
bio, which would prevent us from having to duplicated entries...





Also, should I svn-buildpackage now or am I done ?

Please try whether the package builds nicely.  It is a good idea
to doe this with pdebuild to make sure that all build-depends are
correct.  I will check the package and will upload or come back
to you with some things that should be changed.

As promised I had a look into your packaging.  You can find some commits
which I would like you to inspect.  The main thing I fixed was the
debian/watch file that did not worked.  I also bumped debhelper to
version 9 to get automatic hardening options switched on.  If you have
good reasons to stick to version 8 feel free to revert this change.

I'm a bit unsure about the versioned Build-Depends

   libc6-dev (= 2.15)

which is fullfilled in testing and unstable but not in stable.  So may
be your motivation was to make sure people building the package on
stable get an early warning that something will be broken in the build
process?  I did not tried building the package on stable but are you
sure that this is needed?  Moreover I think we can drop the version on
zlib1g-dev which is fullfilled even in oldstable.


I think we could get rid of the version on libc6-dev, I wasn't sure so 
had put my system's version, that was a bad idea.




I have seen that you have written a manpage debian/kissplice.1.
If you call lintian iwth information severity on (-I) you will notice
a spelling error.  Lintian is also reporting missing manpages of the
other tools.  Woould you mind writing also these manpages?


I didn't write manpages for the other executables because they shouldn't 
be called directly from the user. The main executable is actually a 
python script that calls all the other executables in an integrated 
pipeline (with some executions being done in parallel) . I personally 
don't like the multi-binary arch very much but I won't be able to modify 
this right now. I'll talk about that with the upstream team.




Finally the source would be considered as non-free because the source
for doc/user_guide.pdf is missing.  The best way to fix this is to ask
upstream for the LaTeX source of this documentation.  If they do not
want to distribute this source we need to remove the doc from the source
tarball (which would be suboptimal, thought).  Given that upstream is
cooperative the doc should also be installed into the binary package -
just mention it in debian/docs.


I'll add the .tex and add it to the binary package



Finally I added a debian/upstream file[1] containing the publication
data.  BTW, you can find a skeleton for an upstream file (as well as
most other files adapted for Debian Med - so you do not need to deal
with dh-make boilerplates) in SVN[2].

Kind regards

   Andreas.

[1] https://wiki.debian.org/UpstreamMetadata
[2] svn://svn.debian.org/svn/debian-med/trunk/package_template



Thanks a lot !
David



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Re: Introduction

[Andreas Tille]

Hi David,

On Fri, Jun 21, 2013 at 10:37:50AM +0200, David Parsons wrote:
 
 I won't be of a great help for splitting the set of biological
 packages since I'm not a biologist either.
 I had a question regarding the metapackages (MP for short) however.
 Can a MP be included in another MP ? If so bio-ngs could be a
 dependency of bio, which would prevent us from having to duplicated
 entries...

The idea is not new because it came up in the Debian Science Blend when
there was some interest to include Debian Med's biology packages and
DebiChem packages.  However it is not yet implemented (for several
reasons - the main one probably lack of time).
 
libc6-dev (= 2.15)
 
 which is fullfilled in testing and unstable but not in stable.  So may
 be your motivation was to make sure people building the package on
 stable get an early warning that something will be broken in the build
 process?  I did not tried building the package on stable but are you
 sure that this is needed?  Moreover I think we can drop the version on
 zlib1g-dev which is fullfilled even in oldstable.
 
 I think we could get rid of the version on libc6-dev, I wasn't sure
 so had put my system's version, that was a bad idea.

Probably not bad - just unnecessary.  There are only very few cases
where a versioned libc6-dev is needed.  I do not know any such case in
Debian Med scope.

 I have seen that you have written a manpage debian/kissplice.1.
 If you call lintian iwth information severity on (-I) you will notice
 a spelling error.  Lintian is also reporting missing manpages of the
 other tools.  Woould you mind writing also these manpages?
 
 I didn't write manpages for the other executables because they
 shouldn't be called directly from the user. The main executable is
 actually a python script that calls all the other executables in an
 integrated pipeline (with some executions being done in parallel) .
 I personally don't like the multi-binary arch very much but I won't
 be able to modify this right now. I'll talk about that with the
 upstream team.

The best way to fix this would be to move the binaries in question
to /usr/lib/kissplice and adapt the PATH inside the main program.
Given the fact that it is somehow about esthetics I would not call
this a stumbling stone for a first upload, but it would be nice to
have a better design.

 Finally the source would be considered as non-free because the source
 for doc/user_guide.pdf is missing.  The best way to fix this is to ask
 upstream for the LaTeX source of this documentation.  If they do not
 want to distribute this source we need to remove the doc from the source
 tarball (which would be suboptimal, thought).  Given that upstream is
 cooperative the doc should also be installed into the binary package -
 just mention it in debian/docs.
 
 I'll add the .tex and add it to the binary package

It only needs to be inside the *source* package.  It is sufficient to
ship (even the prebuilded) PDF inside the binary, but the source simply
needs to exist.

 Thanks a lot !

You are welcome

   Andreas.

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Re: Introduction

[David Parsons]

Hi again,

I've just commited the changes, pdebuild looks OK, although it does 
complain about some hooks not being found.


I'll be away for two weeks so don't take it personally if I don't answer 
;-)


David


Le 21/06/2013 11:41, Andreas Tille a écrit :

Hi David,

On Fri, Jun 21, 2013 at 10:37:50AM +0200, David Parsons wrote:

I won't be of a great help for splitting the set of biological
packages since I'm not a biologist either.
I had a question regarding the metapackages (MP for short) however.
Can a MP be included in another MP ? If so bio-ngs could be a
dependency of bio, which would prevent us from having to duplicated
entries...

The idea is not new because it came up in the Debian Science Blend when
there was some interest to include Debian Med's biology packages and
DebiChem packages.  However it is not yet implemented (for several
reasons - the main one probably lack of time).
  

   libc6-dev (= 2.15)

which is fullfilled in testing and unstable but not in stable.  So may
be your motivation was to make sure people building the package on
stable get an early warning that something will be broken in the build
process?  I did not tried building the package on stable but are you
sure that this is needed?  Moreover I think we can drop the version on
zlib1g-dev which is fullfilled even in oldstable.

I think we could get rid of the version on libc6-dev, I wasn't sure
so had put my system's version, that was a bad idea.

Probably not bad - just unnecessary.  There are only very few cases
where a versioned libc6-dev is needed.  I do not know any such case in
Debian Med scope.


I have seen that you have written a manpage debian/kissplice.1.
If you call lintian iwth information severity on (-I) you will notice
a spelling error.  Lintian is also reporting missing manpages of the
other tools.  Woould you mind writing also these manpages?

I didn't write manpages for the other executables because they
shouldn't be called directly from the user. The main executable is
actually a python script that calls all the other executables in an
integrated pipeline (with some executions being done in parallel) .
I personally don't like the multi-binary arch very much but I won't
be able to modify this right now. I'll talk about that with the
upstream team.

The best way to fix this would be to move the binaries in question
to /usr/lib/kissplice and adapt the PATH inside the main program.
Given the fact that it is somehow about esthetics I would not call
this a stumbling stone for a first upload, but it would be nice to
have a better design.


Finally the source would be considered as non-free because the source
for doc/user_guide.pdf is missing.  The best way to fix this is to ask
upstream for the LaTeX source of this documentation.  If they do not
want to distribute this source we need to remove the doc from the source
tarball (which would be suboptimal, thought).  Given that upstream is
cooperative the doc should also be installed into the binary package -
just mention it in debian/docs.

I'll add the .tex and add it to the binary package

It only needs to be inside the *source* package.  It is sufficient to
ship (even the prebuilded) PDF inside the binary, but the source simply
needs to exist.


Thanks a lot !

You are welcome

Andreas.




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Re: Introduction

[Andreas Tille]

Hi David,

On Mon, Jun 17, 2013 at 11:59:26PM +0200, Andreas Tille wrote:
  I suppose I've misunderstood something. Am I not supposed to add
  the package to the “task”file where it fits the best ?
 
 Don't worry - I can easily add it.  You are no member of the Blends team
 which is no real harm if you just want to add this single package - I'll
 do it tomorrow.

Done to bio and bio-ngs.  Remark:  Bio-ngs is currently a subset of bio
which is only rendered at the web pages but not turned into a
metapackage.  This is somehow questionable but we did not yet found a
reasonable solution how to reasonably split up the whole set of
biological packages.  I personally feel unable to do this in a
reasonable manner because I'm no biologist (I'm physicist by profession)
and so far nobody took over the work to find a reasonable split.  The
bio-ngs and bio-phylogeny tasks are some first try to experiment with
some more fine grained tasks but if we miss to inject a package into
(main) bio it will not create a metapackage dependency.  Feel free to
make some suggestions how we could enhance this situation.

  Also, should I svn-buildpackage now or am I done ?
 
 Please try whether the package builds nicely.  It is a good idea
 to doe this with pdebuild to make sure that all build-depends are
 correct.  I will check the package and will upload or come back
 to you with some things that should be changed.

As promised I had a look into your packaging.  You can find some commits
which I would like you to inspect.  The main thing I fixed was the
debian/watch file that did not worked.  I also bumped debhelper to
version 9 to get automatic hardening options switched on.  If you have
good reasons to stick to version 8 feel free to revert this change.

I'm a bit unsure about the versioned Build-Depends

  libc6-dev (= 2.15)

which is fullfilled in testing and unstable but not in stable.  So may
be your motivation was to make sure people building the package on
stable get an early warning that something will be broken in the build
process?  I did not tried building the package on stable but are you
sure that this is needed?  Moreover I think we can drop the version on
zlib1g-dev which is fullfilled even in oldstable.

I have seen that you have written a manpage debian/kissplice.1.
If you call lintian iwth information severity on (-I) you will notice
a spelling error.  Lintian is also reporting missing manpages of the
other tools.  Woould you mind writing also these manpages?

Finally the source would be considered as non-free because the source
for doc/user_guide.pdf is missing.  The best way to fix this is to ask
upstream for the LaTeX source of this documentation.  If they do not
want to distribute this source we need to remove the doc from the source
tarball (which would be suboptimal, thought).  Given that upstream is
cooperative the doc should also be installed into the binary package -
just mention it in debian/docs.

Finally I added a debian/upstream file[1] containing the publication
data.  BTW, you can find a skeleton for an upstream file (as well as
most other files adapted for Debian Med - so you do not need to deal
with dh-make boilerplates) in SVN[2].

Kind regards

  Andreas.

[1] https://wiki.debian.org/UpstreamMetadata
[2] svn://svn.debian.org/svn/debian-med/trunk/package_template

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Re: Introduction

[David Parsons]

Hi Andreas and list,

I've just svn-injected the kissplice package into the SVN repo.
I also tried to update the bio-ngs task file from 
svn.debian.org/svn/blends/projects/med/trunk/debian-med/tasks but got 
the following:

Transmission des données .svn: Échec de la propagation (commit), détails :
svn: Can't create directory '/svn/blends/db/transactions/3807-1.txn': 
Permission denied


I suppose I've misunderstood something. Am I not supposed to add the 
package to the “task”file where it fits the best ?


Also, should I svn-buildpackage now or am I done ?

Thx
David


Le 06/06/2013 13:08, Andreas Tille a écrit :

Hi David,

On Thu, Jun 06, 2013 at 11:53:56AM +0200, David Parsons wrote:

Hi all,

I am new to the debian-med poject and was hinted to introduce myself here.

I'm a french engineer/researcher in bioinformatics and computational
biology.
My main interests are about Evolution and its dynamics but I'm also
involved in sequence analysis and image analysis projects.

Thanks for the introduction.


For now, I have just finished (or so it looks) to package kissplice,
an RNA-seq data analysis tool (more info on
http://kissplice.prabi.fr/) and I would like to make it available on
official repositories.

Please let us know if you might have any trouble to use Debian Med VCS
(Git or SVN at your preference).  We will notice your commits and will
sponsor your package to the Debian mirror once you consider it ready.


Thank you for welcoming me into this group

You are welcome ;-)

  Andreas.

PS: Usually we do not use CC on Debian lists - I just did so because
 I was not sure whether you are subscribed yet.  In future we will
 drop the CC (except if explicitly asked not to)




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Re: Introduction

[Andreas Tille]

Hi David,

On Mon, Jun 17, 2013 at 04:20:54PM +0200, David Parsons wrote:
 Hi Andreas and list,
 
 I've just svn-injected the kissplice package into the SVN repo.

I've noticed the commit - thanks for your work on this.

 I also tried to update the bio-ngs task file from
 svn.debian.org/svn/blends/projects/med/trunk/debian-med/tasks but
 got the following:
 Transmission des données .svn: Échec de la propagation (commit), détails :
 svn: Can't create directory
 '/svn/blends/db/transactions/3807-1.txn': Permission denied

 I suppose I've misunderstood something. Am I not supposed to add
 the package to the “task”file where it fits the best ?

Don't worry - I can easily add it.  You are no member of the Blends team
which is no real harm if you just want to add this single package - I'll
do it tomorrow.

 Also, should I svn-buildpackage now or am I done ?

Please try whether the package builds nicely.  It is a good idea
to doe this with pdebuild to make sure that all build-depends are
correct.  I will check the package and will upload or come back
to you with some things that should be changed.

Kind regards and thanks again for your work

  Andreas.

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Re: Introduction

[Andreas Tille]

Hi David,

On Thu, Jun 06, 2013 at 11:53:56AM +0200, David Parsons wrote:
 Hi all,
 
 I am new to the debian-med poject and was hinted to introduce myself here.
 
 I'm a french engineer/researcher in bioinformatics and computational
 biology.
 My main interests are about Evolution and its dynamics but I'm also
 involved in sequence analysis and image analysis projects.

Thanks for the introduction.

 For now, I have just finished (or so it looks) to package kissplice,
 an RNA-seq data analysis tool (more info on
 http://kissplice.prabi.fr/) and I would like to make it available on
 official repositories.

Please let us know if you might have any trouble to use Debian Med VCS
(Git or SVN at your preference).  We will notice your commits and will
sponsor your package to the Debian mirror once you consider it ready.

 Thank you for welcoming me into this group

You are welcome ;-)

 Andreas.

PS: Usually we do not use CC on Debian lists - I just did so because
I was not sure whether you are subscribed yet.  In future we will
drop the CC (except if explicitly asked not to) 

-- 
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Introduction.

[Diane Trout]

Hello,

Steffen Möller suggested I introduce myself.

I'm a software developer / system administrator working in the Wold Lab at the 
California Institute of Technology. The lab's focus is on genome scale 
transcription regulation. My current main job duties are dealing with tracking 
and submitting the high-throughput sequence.

My background is in CS and not biology, most of my coding experience is in 
python, although I can code in C++ and C. I first started using Debian a bit 
before 1998. I have been using Ubuntu for the past few years. (Though I am 
bothered by their decision to monitize their users though in-OS advertisements).

Diane


pgpeUraeac1VM.pgp
Description: PGP signature

Introduction

[Florent Angly]

Dear DebianMed list,

I just joined the group. I am a computational biologist, a microbial 
ecologist specifically, who uses mostly Perl when coding. I have been 
using Debian-based Linux distros for quite some time (Linux Mint Debian 
Edition at the moment) and became interested in packaging software for 
Debian.


I maintain a few Perl modules on CPAN (http://search.cpan.org/~fangly/ 
http://search.cpan.org/%7Efangly/) and have recently uploaded my first 
deb package, Math::Random::MT::Perl, at 
http://mentors.debian.net/package/libmath-random-mt-perl-perl. I have 
also joined the Debian Perl group.


DebianMed has already packaged great programs that are useful to 
microbial ecologists (e.g. QIIME, Velvet). There are other ones that 
could be useful and that I could try to package. For example, MetaVelvet 
is an assembler specific to metagenomic datasets (but I do not know if 
is mature enough for packaging yet). Another example is Grinder 
(http://sourceforge.net/projects/biogrinder/) software to simulate 
amplicon and shotgun datasets.


Thanks for letting me join the group and best regards,

Florent

Re: Introduction

[Andreas Tille]

Hi Florent,

On Fri, Dec 30, 2011 at 09:24:19PM +1000, Florent Angly wrote:
 I maintain a few Perl modules on CPAN
 (http://search.cpan.org/~fangly/
 http://search.cpan.org/%7Efangly/) and have recently uploaded my
 first deb package, Math::Random::MT::Perl, at
 http://mentors.debian.net/package/libmath-random-mt-perl-perl. I
 have also joined the Debian Perl group.

While it is perfectly fine to maintain perl packages inside the Debian
Perl group (we are not competing each other about maintaining certain
packages) just tell us if you need a sponsor if needed.
 
 DebianMed has already packaged great programs that are useful to
 microbial ecologists (e.g. QIIME, Velvet). There are other ones that
 could be useful and that I could try to package. For example,
 MetaVelvet is an assembler specific to metagenomic datasets (but I
 do not know if is mature enough for packaging yet). Another example
 is Grinder (http://sourceforge.net/projects/biogrinder/) software to
 simulate amplicon and shotgun datasets.

Just let us know if you might face any blockers or need sponsors.
The rules should be layed out in Debian Med policy document.
 
 Thanks for letting me join the group and best regards,

Welcome in the team

  Andreas.

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Removed plain uncompiled c++ code from ensembl binary (Was: new member introduction)

[Andreas Tille]

On Fri, Dec 09, 2011 at 01:00:48PM +, Nick James wrote:
 I'm tempted to kick all files matching *.h and *.cpp from the binary
 package where these are pretty useless.  This would solve the lintian
 warnings
 
 W: libensembl-core-perl: executable-not-elf-or-script 
 usr/share/ensembl/ensembl/misc-scripts/alternative_splicing/AltSplicingToolkit/src/util/StringUtil.h
 W: libensembl-core-perl: executable-not-elf-or-script 
 usr/share/ensembl/ensembl/misc-scripts/alternative_splicing/AltSplicingToolkit/src/util/StringUtil.cpp
 
 What do you think?
 This is used for loading data into ensembl again, and is not needed
 for the functioning website ( as with run_me in the previous post).
 However, this would be a useful resource for anyone wanting to load
 variation data into their own copy of Ensembl, so I think it should
 be kept in some form. I think you mean just keep the binaries and
 not the source, right?

I investigated things a bit and realised that the binary in this
subdirectory is actually not builded at all in our current packaging.
So either this was intended and thus correct we do not need the sources
in some hidden place in the binary or we just need to find a way how
to properly build the resulting binary.  I just implemented the first
variant (because it's more simple) in

http://anonscm.debian.org/viewvc/debian-med/trunk/packages/ensembl/ensembl/trunk/debian/rules?r1=8979r2=8980;

What do you think?

BTW, a very valuable thing to do would be to write a man page for

  ensembl-bin: binary-without-manpage usr/bin/calc_genotypes

If you have no idea how to do this just say so - there are some hints
how to do this for a start.  YOu will also find a lot of examples in
Debian Med SVN via

  find trunk/packages -name *.[1-9]

We might make upstream happy (and thus they might be more easier willing
to accept other patches) if we provide them this piece of documentation.

Kind regards

   Andreas.

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Re: new member introduction

[Nick James]

Hi Andreas,

On 08/12/11 21:56, Andreas Tille wrote:

Hi again,

On Thu, Dec 08, 2011 at 10:02:13PM +0100, Andreas Tille wrote:

Hi Nick,

On Thu, Dec 08, 2011 at 05:24:51PM +, Nick James wrote:

It is what the Ensembl
team use internally for batch submission.

Iven in this case the script looks somehow suspicious.

s/I/E/

Nick, if you wonder how to remove the script from the package you might
like to inspect either


http://anonscm.debian.org/viewvc/debian-med?view=revisionsortby=revrevision=8847

or


http://lists.alioth.debian.org/pipermail/debian-med-commit/2011-December/010208.html

at your preference.  You see in the debian/rules script is done most of
the work.  However, typical rules scripts are way more easy.  The
Ensembl one is that complex because of two reasons:

   1. Several non-conformant scripts regarding pathes and permissions
   2. No proper Makefile with install target


My suggestion is that we just ignore this script as it is not needed
for Ensembl to run.

Thanks for the hint.  Could you spot more such stuff which is not
needed to run?

I'm tempted to kick all files matching *.h and *.cpp from the binary
package where these are pretty useless.  This would solve the lintian
warnings

W: libensembl-core-perl: executable-not-elf-or-script 
usr/share/ensembl/ensembl/misc-scripts/alternative_splicing/AltSplicingToolkit/src/util/StringUtil.h
W: libensembl-core-perl: executable-not-elf-or-script 
usr/share/ensembl/ensembl/misc-scripts/alternative_splicing/AltSplicingToolkit/src/util/StringUtil.cpp

What do you think?
This is used for loading data into ensembl again, and is not needed for 
the functioning website ( as with run_me in the previous post). However, 
this would be a useful resource for anyone wanting to load variation 
data into their own copy of Ensembl, so I think it should be kept in 
some form. I think you mean just keep the binaries and not the source, 
right?


Thanks,

Nick

Kind regards

Andreas.





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Re: new member introduction

[Andreas Tille]

On Fri, Dec 09, 2011 at 01:00:48PM +, Nick James wrote:
 W: libensembl-core-perl: executable-not-elf-or-script 
 usr/share/ensembl/ensembl/misc-scripts/alternative_splicing/AltSplicingToolkit/src/util/StringUtil.h
 W: libensembl-core-perl: executable-not-elf-or-script 
 usr/share/ensembl/ensembl/misc-scripts/alternative_splicing/AltSplicingToolkit/src/util/StringUtil.cpp
 
 What do you think?
 This is used for loading data into ensembl again, and is not needed
 for the functioning website ( as with run_me in the previous post).
 However, this would be a useful resource for anyone wanting to load
 variation data into their own copy of Ensembl, so I think it should
 be kept in some form. I think you mean just keep the binaries and
 not the source, right?

For sure I would keep the compiled binary if it makes sense.  Otherwise
if the source would be usefull for the end user I would rather move it
to some place like

/usr/share/doc/ensembl/examples/some-reasonable-name/*.[ch]

to teach users about the chance to do usefull stuff with C code.

For a quick check I did a

   find . -name *.cpp | grep -v /doc/

and found some hits.  About 50% are from ensembl and I'd regard these
files in this location as pretty useless for the user.  IMHO anything
which is residing in directories named /src/ inside the source tree
should not make its way into the binary package (at least not in the way
it is done now).

Kind regards

Andreas.

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Re: new member introduction

[Nick James]

Hi Andreas,

Thanks for the instructions.  One question, should I be checking out the 
source with write permission:


*svn co*  |svn+ssh://u...@svn.debian.org/svn/debian-med/trunk/...
in which case do I need a username / password? And commit changes myself.

Or just for reading:
|*svn co*  |svn://svn.debian.org/debian-med/trunk/...

then build and test and feedback suggestions to you?

Thanks,

Nick
|



On 09/12/11 13:02, Andreas Tille wrote:

On Fri, Dec 09, 2011 at 11:55:41AM +, Nick James wrote:

I'm happy to look into other things that you are not sure if they
are needed.  How do I get a list of scripts that are causing
problems?

The idea is to run lintian on the resulting packages.  So how to get
these packages.  There are (at least) two ways:

   A. The brave way to build it yourself doing the following:

 1. Checkout either full Debian Med SVN or just the tree for
ensembl (just ask for more details if policy is not clear
about how to do this)
 2. cd into the packaging root directory (where the debian/
directory is sitting but *not* into the debian/ dir)
 3. make -f debian/rules get-orig-source
will create the source tarball I'm working on
 4. Build the package which also has some variants.  Policy
recommends svn-buildpackage.  If it works for you that's
fine.  I personally use pbuilder directly which does the
building of the packages in a chroot which needs to be
created using `sudo pbuilder --create`.  Pbuilder is an
important technique you need to understand sooner or later.
In this specific case it is better to do it sooner because
for a reason I did not found for the moment ensembl will
not build twice in a row when using simple debuild (which
is the simplest method to build the package I could
imagine).  This does not build twice in a row needs
further fixing - I have no idea why this happens because
all changes of files happen in a separate dir but somehow
original sources are touched.

In short:  Decide between
  svn-buildpackage
  pdebuild
  debuild
to create the packages.
 5. Once you created the packages you can run

  lintian *.dsc *.deb

to have a simple list of critical things.  For a newcommer
it is better to run

  lintian -i *.dsc *.deb

which gives additional explanations.
And we have the nitpicking mode:

  lintian -i -I *.dsc *.deb

So you get the scripts which are technically problematic.


There are a lot of scripts like this one, so I don't want
to go through them all unless really necessary! Many of them are
useful too.

Well, this is a matter of *content*.  No automatic test can detect this.
We just went by random in something which was not usefull inside the
package *and* technically incorrect.  Perhaps you might look for file
types which do not need to end up in an end user package.  As I suggested
pure source code files like *.c, *.cpp and *.h do not really belong into
this.  Perhaps you might see other file types as well.

Hint: I personally like to use MidnightCommander to browse inside Debian
packages - perhaps you like this tool as well.

Hope this helps.  Feel free to keep on asking - I'll be offline over the
weekend, but others might step in as well for basic packaging questions.

Kind regards

 Andreas.

Re: new member introduction

[Andreas Tille]

On Fri, Dec 09, 2011 at 04:56:11PM +0100, Steffen Möller wrote:
 On 12/09/2011 02:02 PM, Andreas Tille wrote:
  On Fri, Dec 09, 2011 at 11:55:41AM +, Nick James wrote:
  I'm happy to look into other things that you are not sure if they
  are needed.
 A major reason for Ensembl to remain in the (not so fancy)
 experimental section is for its dependency on bioperl 1.2.3,
 which itself is in experimental. Since so many have lost some
 tooth over this already, while I am confident that this will
 eventually be resolved, it will take a while. So the Ensembl
 package will remain in experimental that long at least.

That's a fair reason to use experimental.  Perhaps somebody with access
to Ensembl bugtracker might open another ticket (in comparison ton
libwww-perl.
 
 One of those other things coming to mind is the Jalview
 .jar file shipping with the Ensembl sources. My understanding is
 that this was an old version of Jalview, after all it did not need
 any dependencies. Andreas has now, to comply with the GPL
 with no extra effort, substitutede it with the very recent Jalview
 that now (thanks to Vincent and Jim) ships with Debian. This
 was not so much on my agenda, but maybe you could check
 if this new version of Jalview does not have an API change
 effecting Ensembl too much?

Because this is definitely helpful it might make sense if I upload
a preliminary package to my people.debian.org area to enable easy
download of the packages for testing.  I'll do so next week.
 
Kind regards

  Andreas. 

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new member introduction

[Nick James]

Hi,

Just a quick post to introduce myself.

I work for Eagle Genomics, an outsourced bioinformatics services and 
software company specialising in genome content management and the 
provision of open-source solutions.


At Eagle we are intestered in packaging Ensembl, which is widely used 
genome browser and annotation software.  I am very new to packaging.  
However, I have been an ubuntu and Ensembl user for many years.  So I 
think to start with my involvement will be to help solve any 
Ensembl-related packaging problems, and then later to develop my own 
packaging skills.


Thanks,

Nick James
Eagle Genomics Ltd.




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Re: new member introduction

[Andreas Tille]

Hi Nick,

On Thu, Dec 08, 2011 at 03:56:20PM +, Nick James wrote:
 Just a quick post to introduce myself.
 ...

welcome in the team.  I think I had your address in CC in my mail
yesterday concerning some Ensembl issues.  It would be great if you
could contact Ensembl authors about this.  I hope you feel comfortable
with all the docs I just recommended - feel free to ask any question
here.

Kind regards and thanks for the introduction

Andreas.

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Re: new member introduction

[Nick James]

Hi Andreas,

You probably know this, but bsub is the submission command for the LSF 
computer cluster submission software. It is what the Ensembl team use 
internally for batch submission.


My point is that there are many utility scripts ( like 
ensembl-variation/scripts/import/run.me ) hanging about in the ensembl 
code that are not needed at all in order to have a fully functioning 
website and API code.  They are only used internally by the Ensembl team 
as they develop new data for a new release. As they are only intended 
for internal use they tend to be very tied to the exact platform they 
develop on ( in this case LSF, with perl in /usr/local/ensembl/bin/perl 
and a shared dir on /ecs2/scratch3/ ).


My suggestion is that we just ignore this script as it is not needed for 
Ensembl to run.


Thanks,

Nick

On 08/12/11 16:26, Andreas Tille wrote:

Hi Nick,

On Thu, Dec 08, 2011 at 03:56:20PM +, Nick James wrote:

Just a quick post to introduce myself.
...

welcome in the team.  I think I had your address in CC in my mail
yesterday concerning some Ensembl issues.  It would be great if you
could contact Ensembl authors about this.  I hope you feel comfortable
with all the docs I just recommended - feel free to ask any question
here.

Kind regards and thanks for the introduction

 Andreas.




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Ensembl with Debian Re: new member introduction

[Steffen Möller]

Hello,

On 12/08/2011 06:24 PM, Nick James wrote:
 My suggestion is that we just ignore this script as it is not needed
 for Ensembl to run.
We should decide over time what it means for us to see Ensembl run.
The current definition for our package seems to be use the public data
of Ensembl but have a local user management. This makes some very
decent sense for anyone interested in learning or extending the
functionality of Ensembl from day one. And with so many other
bioinformatics and statistical tools available in Debian, there is
plenty of opportunity for everyone to investigate so many different things.

To me, having Ensembl in and so many complete genomes with it, or at
least accessible through it, this is the twilight of Open Source and
Citizen Science. And when we manage to have it all prepared for
technical enthusiasts, we have also prepared it for the technically
enthused clinician. They exist - some of them I talk to every day. What
happens then - in terms of funding and ideas - we do not know.

From what I grasped, EagleGenomics is excellent in bringing newly
sequenced individuals (patients) or pools of such (pathogens) into
Ensembl. This means assembly, annotation and comparisons of the
sequences. We can as a community learn a lot from their selection of
tools for the job and all the scripts they use to perform and control
the process. I hope Debian to continue to be important for them and to
see Nick and his colleagues help developing Debian further for their
immediate needs, and for the long term benefit of us all.

Good you are around. Many thanks and regards,

Steffen



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Re: new member introduction

[Andreas Tille]

Hi Nick,

On Thu, Dec 08, 2011 at 05:24:51PM +, Nick James wrote:
 You probably know this, but bsub is the submission command for the
 LSF computer cluster submission software.

Well, please do not overestimate my knowledge.  I did not worked with
clusters so far.

 It is what the Ensembl
 team use internally for batch submission.

Iven in this case the script looks somehow suspicious.
 
 My point is that there are many utility scripts ( like
 ensembl-variation/scripts/import/run.me ) hanging about in the
 ensembl code that are not needed at all in order to have a fully
 functioning website and API code.  They are only used internally by
 the Ensembl team as they develop new data for a new release. As they
 are only intended for internal use they tend to be very tied to the
 exact platform they develop on ( in this case LSF, with perl in
 /usr/local/ensembl/bin/perl and a shared dir on /ecs2/scratch3/ ).
 
 My suggestion is that we just ignore this script as it is not needed
 for Ensembl to run.

Thanks for the hint.  Could you spot more such stuff which is not
needed to run?

Kind regards

  Andreas.

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Re: Ensembl with Debian Re: new member introduction

[Andreas Tille]

On Thu, Dec 08, 2011 at 07:43:25PM +0100, Steffen Möller wrote:
 We should decide over time what it means for us to see Ensembl run.
 The current definition for our package seems to be use the public data
 of Ensembl but have a local user management. This makes some very
 decent sense for anyone interested in learning or extending the
 functionality of Ensembl from day one. And with so many other
 bioinformatics and statistical tools available in Debian, there is
 plenty of opportunity for everyone to investigate so many different things.

While I agree with you that there are a plenty of different use cases it
was always good style in Debian to provide a pure use package and a
development package in addition.  For the moment I would concentrate
on the first part.  Considering the fact that we do not have bsub in
Debian anyway the script in question does not (yet) qualify for any of
these flowers.
 
 Good you are around. Many thanks and regards,

Yes, definitely.

Kind regards

 Andreas. 

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New member introduction

[Olivier Langella]

Hello,

I am new to debian-med and I would like to introduce myself :
Bioinformatics engineer in the UMR de Génétique Végétale 
(http://moulon.inra.fr/welcomegb.html) and Linux user since the Debian 
Potato release, I would be happy to contribute to this great project 
(depending on my skills).


I've developed some populations genetic softwares such as populations 
(http://bioinformatics.org/~tryphon/populations/) or treeplot. I will 
first try to help Charles Plessy and Vincent Danjean to clean treeplot 
sources to make a debian package.


thanks for all the work the debian-med team has made to provide so much 
biological/medical softwares,


Olivier Langella


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GSoC Student Introduction

[Ignacio Vergara]

Hi

I'm Ignacio Vergara, a prospective GSoC student. My proposal is about a
biological database manager.

Any suggestion is welcomed.

Ignacio