Re: Bio-Linux

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Re: Bio-Linux

Andreas Tille-5
[Got confirmation from William to quote him in public - please
everybody rise your opinion here.  Thank you.]

----- Forwarded message from Andreas Tille <[hidden email]> -----

Hi William,

On Thu, Jul 26, 2018 at 05:50:52PM +0100, William McCaffery wrote:
> I've been working with Tony on Bio-linux 9,

So Tony did not told you that I try to force people to open discussion
on our mailing list? ;-)

Honestly I care a lot for having a public record and keep the team
informed about all issues except really private things and I have quite
some record of shamelessly ignoring the netiquette by simply answering
private mails in public.  Since you are new and I'm not sure whether you
want to see your e-mail address exposed on a publicly archived list this
is just a warning and the question whether you give permission to bounce
my mail to [hidden email] and we keep on discussing there.
Please be aware that I will do this without question in the future for
very good reasons if no private content is in your mail.

> and he mentioned that he had
> planned to base the new package on med-bio. To this end, he suggested I
> asked you about the process of doing this. Tony mentioned that I would have
> to start by submitting a bug report?

Well, you can do a bug report but we can also discuss this on the
mailing list where typically more people pay attention to a topic that
deserves a wider audience.

I can assure you that I very open for integrating Bio-Linux and will
definitely support your attempt.  We just need to find out what might be
the best solution for you.
 
> I also was unsure of how to structure the meta-package. I have read the
> blend documentation, but I am still confused by the structure of the deb-med
> package source.

Good so far.  I suggest you register on Salsa for a login and I will add
you to the Debian Med team to grant you commit permissions to the tasks.

> Am I right in saying that we would only need to change
> debian/control?

Not really.  debian/control is auto-generated.  You might need to create
a new (several new?) tasks biolinux (biolinux-featureA,
biolinux-featureB, ...) and than run `make dist` which will recreate
d/control and adds those task(s) to debian/control.

> I also wanted to consult with you on the best way to fit in
> a bio-linux-desktop meta package, since the package would have an overlap of
> some packages from other meta-packages already within debian-med.

Overlaps are no problem at all.  Tasks are no exclusive categories but
rather sets of packages that are needed for certain tasks.  So don't
mind about this.

> In
> addition to this I am not completely sure how Tony wanted the new package to
> be based on the med-bio package. He said that you discussed this prior; is
> this what he meant? We've been exchanging emails but I'm still a little
> uncertain.

Well, this depends.  If med-bio (and may be med-bio-dev are fine for you
you can simply Depend from these and be done with a zero maintenance
effort.  If we add new packages these will be mentioned there (and I have
also developed tools to verify that everything is really included so you
are safe that no new package will be missing).

So lets discuss this all on the mailing list not wasting input of others
(including Tony's) which have a valuable opinion (specifically since I'm
not a user and thus I'm probably bad in guessing what users really need.

Kind regards

       Andreas.

--
http://fam-tille.de

----- End forwarded message -----

--
http://fam-tille.de

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Re: Bio-Linux

Andreas Tille-5
[ Leaving only the part of your mal that should be discussed in public]

Hi Tony,

On Fri, Jul 27, 2018 at 02:30:56PM +0100, Tony Travis wrote:

> > Well, this depends.  If med-bio (and may be med-bio-dev are fine for you
> > you can simply Depend from these and be done with a zero maintenance
> > effort.  If we add new packages these will be mentioned there (and I have
> > also developed tools to verify that everything is really included so you
> > are safe that no new package will be missing).
>
> I want to create a 'bio-linux-desktop' meta-package with more or less
> the same packages as Bio-Linux 8, but with the packages sourced from
> Debian Sid via the Ubuntu repositories. To that end, I want to use the
> 'med-bio' and 'med-bio-dev' metapackages as a starting point. It is not
> practical, or desirable, to install everything in 'med-bio' onto a
> 'live' DVD/USB iso with a max 4GB payload.

OK, I understood that full med-bio and med-bio-dev are to heavy for a
live system.  Just for my personal understanding:  Is Bio-Linux
targeting at live media *exclusively*?

So we obviously need to maintain separate tasks for bio-linux.  Please
note that the blends-dev scripts are adding a prefix to every single
task so if you create a task bio-linux-desktop the resulting metapackage
will be named med-bio-linux-desktop.  For my feeling this is a bit hard
to read and so I'd rather go with a task desktop-bio-linux but you are
free to decide.

I'd also see an option to maintain a separate set of metapackages.  The
Debian Med team could create another source package called bio-linux.
There you create a task desktop (may be more) and than the resulting
metapackage will be named bio-linux-desktop.  You are free to define
more tasks that will all get the bio-linux prefix in the metapackage
names.  I have not thought longish about this but for the moment I do
not see much extra effort in this.  So feel free to decide what might be
your prefered option.
 
> > So lets discuss this all on the mailing list not wasting input of others
> > (including Tony's) which have a valuable opinion (specifically since I'm
> > not a user and thus I'm probably bad in guessing what users really need.
>
> I'll be driving to Milan next week, so I might not reply to emails for a
> few days - Please do move our conversation over to the Debian-Med list.

Done and have a safe trip

    Andreas.

--
http://fam-tille.de

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Re: Bio-Linux

William-9
In reply to this post by Andreas Tille-5
Hi,

If we were to create a new task within deb-med, would I be correct in
saying that I would have to:

-file a WNPP bug report,

-Create a new task in Debian med in the blends repository

-Add to this task all packages currently in Bio-Linux even if they
aren't currently packaged in sid so that if they are added in the future
the package will work with them without having to update it.

When it's said that we're basing this package on med-bio & med-bio-dev,
does this mean we would be taking the existing tasks for each, merging
them, removing unnecessary packages, then adding the Bio-Linux packages
that were recently added to sid? Would we also include packages not in
sid, but ones that would be considered useful for Bio-Linux, so that we
would not have to update the meta-package again when the packages are
added in the future?

In regards to the suggestion of a separate source package, what would
that involve? Personally I don't think that having the name
med-bio-linux-desktop would be an issue, since, as far as I'm aware the
package will be mainly distributed from within the bio-linux iso,
through download, usb and cd.

Thanks,

William






On 28/07/18 00:18, Andreas Tille wrote:

> [Got confirmation from William to quote him in public - please
> everybody rise your opinion here.  Thank you.]
>
> ----- Forwarded message from Andreas Tille <[hidden email]> -----
>
> Hi William,
>
> On Thu, Jul 26, 2018 at 05:50:52PM +0100, William McCaffery wrote:
>> I've been working with Tony on Bio-linux 9,
> So Tony did not told you that I try to force people to open discussion
> on our mailing list? ;-)
>
> Honestly I care a lot for having a public record and keep the team
> informed about all issues except really private things and I have quite
> some record of shamelessly ignoring the netiquette by simply answering
> private mails in public.  Since you are new and I'm not sure whether you
> want to see your e-mail address exposed on a publicly archived list this
> is just a warning and the question whether you give permission to bounce
> my mail to [hidden email] and we keep on discussing there.
> Please be aware that I will do this without question in the future for
> very good reasons if no private content is in your mail.
>
>> and he mentioned that he had
>> planned to base the new package on med-bio. To this end, he suggested I
>> asked you about the process of doing this. Tony mentioned that I would have
>> to start by submitting a bug report?
> Well, you can do a bug report but we can also discuss this on the
> mailing list where typically more people pay attention to a topic that
> deserves a wider audience.
>
> I can assure you that I very open for integrating Bio-Linux and will
> definitely support your attempt.  We just need to find out what might be
> the best solution for you.
>  
>> I also was unsure of how to structure the meta-package. I have read the
>> blend documentation, but I am still confused by the structure of the deb-med
>> package source.
> Good so far.  I suggest you register on Salsa for a login and I will add
> you to the Debian Med team to grant you commit permissions to the tasks.
>
>> Am I right in saying that we would only need to change
>> debian/control?
> Not really.  debian/control is auto-generated.  You might need to create
> a new (several new?) tasks biolinux (biolinux-featureA,
> biolinux-featureB, ...) and than run `make dist` which will recreate
> d/control and adds those task(s) to debian/control.
>
>> I also wanted to consult with you on the best way to fit in
>> a bio-linux-desktop meta package, since the package would have an overlap of
>> some packages from other meta-packages already within debian-med.
> Overlaps are no problem at all.  Tasks are no exclusive categories but
> rather sets of packages that are needed for certain tasks.  So don't
> mind about this.
>
>> In
>> addition to this I am not completely sure how Tony wanted the new package to
>> be based on the med-bio package. He said that you discussed this prior; is
>> this what he meant? We've been exchanging emails but I'm still a little
>> uncertain.
> Well, this depends.  If med-bio (and may be med-bio-dev are fine for you
> you can simply Depend from these and be done with a zero maintenance
> effort.  If we add new packages these will be mentioned there (and I have
> also developed tools to verify that everything is really included so you
> are safe that no new package will be missing).
>
> So lets discuss this all on the mailing list not wasting input of others
> (including Tony's) which have a valuable opinion (specifically since I'm
> not a user and thus I'm probably bad in guessing what users really need.
>
> Kind regards
>
>         Andreas.
>

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Re: Bio-Linux

Andreas Tille-5
Hi William

On Tue, Jul 31, 2018 at 07:50:12PM +0100, William McCaffery wrote:
> Hi,
>
> If we were to create a new task within deb-med, would I be correct in saying
> that I would have to:
>
> -file a WNPP bug report,

This is only needed for new source packages.  As long as you stick to
debian-med source package there is no need for a WNPP bug.

> -Create a new task in Debian med in the blends repository

Yes.
 
> -Add to this task all packages currently in Bio-Linux even if they aren't
> currently packaged in sid so that if they are added in the future the
> package will work with them without having to update it.

Yes.

> When it's said that we're basing this package on med-bio & med-bio-dev, does
> this mean we would be taking the existing tasks for each, merging them,
> removing unnecessary packages, then adding the Bio-Linux packages that were
> recently added to sid?

I guess you have the least work if you just copy tasks/bio delete what you
do not want and add what's missing.

> Would we also include packages not in sid, but ones
> that would be considered useful for Bio-Linux, so that we would not have to
> update the meta-package again when the packages are added in the future?

Just add what *should* be inside.  The metapackages need to be re-rendered
but that should be no issue.
 
> In regards to the suggestion of a separate source package, what would that
> involve? Personally I don't think that having the name med-bio-linux-desktop
> would be an issue, since, as far as I'm aware the package will be mainly
> distributed from within the bio-linux iso, through download, usb and cd.

So my suggestion is to stick to the debian-med source package since
that's the more simple approach.  In case you might decide otherwise
later I'd volunteer to do some work (which is faster done myself than
drafting a long explanation.

> Thanks,

You are welcome

     Andreas.

--
http://fam-tille.de

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Re: Bio-Linux

Steffen Möller
Heya,

On 8/1/18 11:39 AM, Andreas Tille wrote:

> Hi William
>
> On Tue, Jul 31, 2018 at 07:50:12PM +0100, William McCaffery wrote:
>> Hi,
>>
>> If we were to create a new task within deb-med, would I be correct in saying
>> that I would have to:
>>
>> -file a WNPP bug report,
> This is only needed for new source packages.  As long as you stick to
> debian-med source package there is no need for a WNPP bug.
>
>> -Create a new task in Debian med in the blends repository
> Yes.
>  
>> -Add to this task all packages currently in Bio-Linux even if they aren't
>> currently packaged in sid so that if they are added in the future the
>> package will work with them without having to update it.
> Yes.
>
>> When it's said that we're basing this package on med-bio & med-bio-dev, does
>> this mean we would be taking the existing tasks for each, merging them,
>> removing unnecessary packages, then adding the Bio-Linux packages that were
>> recently added to sid?
> I guess you have the least work if you just copy tasks/bio delete what you
> do not want and add what's missing.
>
>> Would we also include packages not in sid, but ones
>> that would be considered useful for Bio-Linux, so that we would not have to
>> update the meta-package again when the packages are added in the future?
> Just add what *should* be inside.  The metapackages need to be re-rendered
> but that should be no issue.
>  
>> In regards to the suggestion of a separate source package, what would that
>> involve? Personally I don't think that having the name med-bio-linux-desktop
>> would be an issue, since, as far as I'm aware the package will be mainly
>> distributed from within the bio-linux iso, through download, usb and cd.
> So my suggestion is to stick to the debian-med source package since
> that's the more simple approach.  In case you might decide otherwise
> later I'd volunteer to do some work (which is faster done myself than
> drafting a long explanation.
>
>> Thanks,
> You are welcome
>
>      Andreas.

I like that approach. We should possibly discuss this also on the Debian
Derivatives list.

https://lists.debian.org/debian-derivatives/

Cheers,

Steffen



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Re: Bio-Linux

Tony Travis
In reply to this post by Andreas Tille-5
On 28/07/18 00:45, Andreas Tille wrote:
> [...]
> OK, I understood that full med-bio and med-bio-dev are to heavy for a
> live system.  Just for my personal understanding:  Is Bio-Linux
> targeting at live media *exclusively*?

Hi, Andreas.

Not exclusively, the "Bio-Linux" project has two objectives:

1. Povide a 'live' DVD/USB environment that can be used to learn about
bioinformatics on a modest PC/laptop with the NEBC training materials.

2. Install "Bio-Linux" permanently to the same PC, or a more powerful
server. I've installed all of my "Bio-Linux" terminal servers from the
same 'live' USB and added software not on the 'live' .iso from the
repositories that are pre-configured in "Bio-Linux".

> So we obviously need to maintain separate tasks for bio-linux.  Please
> note that the blends-dev scripts are adding a prefix to every single
> task so if you create a task bio-linux-desktop the resulting metapackage
> will be named med-bio-linux-desktop.  For my feeling this is a bit hard
> to read and so I'd rather go with a task desktop-bio-linux but you are
> free to decide.

I guess you would like to drop the redundant "-bio-linux" and call it
"med-bio-desktop", which is not an unreasonable suggestion because  we
are actually discussing a sub-set of "med-bio" that contains most of the
packages present in "Bio-Linux" and the possibility of adding missing
packages to "med-bio". Logically, we could also create "med-bio-server"
so that some of the 'server' side of "Bio-Linux" can be removed from the
'live' desktop: A typical install would then be server + desktop.

> I'd also see an option to maintain a separate set of metapackages.  The
> Debian Med team could create another source package called bio-linux.
> There you create a task desktop (may be more) and than the resulting
> metapackage will be named bio-linux-desktop.  You are free to define
> more tasks that will all get the bio-linux prefix in the metapackage
> names.  I have not thought longish about this but for the moment I do
> not see much extra effort in this.  So feel free to decide what might be
> your prefered option.

I really appreciate the help and support of the Debian-Med team and I
think it would be very good idea to create a new source package called
"bio-linux" if you are all willing to help? Steffen also mentioned in
Barcelona, that a 'live' distro using packages from the Debian-Med team
would help to raise the profile of the Debian-Med

>>> So lets discuss this all on the mailing list not wasting input of others
>>> (including Tony's) which have a valuable opinion (specifically since I'm
>>> not a user and thus I'm probably bad in guessing what users really need.
>>
>> I'll be driving to Milan next week, so I might not reply to emails for a
>> few days - Please do move our conversation over to the Debian-Med list.
>
> Done and have a safe trip

Thanks, I arrived safely in Milan with eleven servers, a 19" rack in a
flat-pack and a huge pile of other kit last night :-)

I'll be working here in Milan until Fri 10 Aug, then I'll be driving
back home on holiday through France with very infrequent access to the
Internet until 11 Sep.

Bye,

  Tony.

--
Minke Informatics Limited, Registered in Scotland - Company No. SC419028
Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK)
tel. +44(0)19755 63548                    http://minke-informatics.co.uk
mob. +44(0)7985 078324        mailto:[hidden email]

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Re: Bio-Linux

Tony Travis
In reply to this post by William-9
On 31/07/18 19:50, William McCaffery wrote:
> [...]
> In regards to the suggestion of a separate source package, what would
> that involve? Personally I don't think that having the name
> med-bio-linux-desktop would be an issue, since, as far as I'm aware the
> package will be mainly distributed from within the bio-linux iso,
> through download, usb and cd.

Hi, William.

I think it is an issue, because I'd like to install "bio-linux-desktop"
on an existing Ubuntu/Debian system using:

  apt install bio-linux-desktop

I'd also like "bio-linux server", so the server-side can be removed from
the desktop. In principle I'd like to install everything using:

  apt install bio-linux

As you can install all of "med-bio" using:

  apt install med-bio

Bye,

  Tony.

--
Minke Informatics Limited, Registered in Scotland - Company No. SC419028
Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK)
tel. +44(0)19755 63548                    http://minke-informatics.co.uk
mob. +44(0)7985 078324        mailto:[hidden email]

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Re: Bio-Linux

William-9
Hi Tony,

That sounds reasonable, especially if we want to keep them as discreet
projects. If Andreas would be willing to set this up that would be great.

As far as I can tell from the Debian documentation and what we've
discussed, the complete set of Bio-Linux tasks would simply be Tim's
original package list, divided into desktop and server tasks. I would
ask your preference on whether we would use the reduced list I created
which only has packages in sid (although this has some issues with
virtual packages) or the compete set. I know that the documentation
states the latter, but I don't know if all of the packages are still
useful to Bio-Linux. As  for separating Bio-Linux server and client
packages, I can go through Tim's packages and try and create a list of
packages for a server task for review.

thanks,

William


On 03/08/18 12:11, Tony Travis wrote:

> On 31/07/18 19:50, William McCaffery wrote:
>> [...]
>> In regards to the suggestion of a separate source package, what would
>> that involve? Personally I don't think that having the name
>> med-bio-linux-desktop would be an issue, since, as far as I'm aware the
>> package will be mainly distributed from within the bio-linux iso,
>> through download, usb and cd.
> Hi, William.
>
> I think it is an issue, because I'd like to install "bio-linux-desktop"
> on an existing Ubuntu/Debian system using:
>
>    apt install bio-linux-desktop
>
> I'd also like "bio-linux server", so the server-side can be removed from
> the desktop. In principle I'd like to install everything using:
>
>    apt install bio-linux
>
> As you can install all of "med-bio" using:
>
>    apt install med-bio
>
> Bye,
>
>    Tony.
>

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Re: Bio-Linux

Andreas Tille-5
Hi William and Tony,

On Fri, Aug 03, 2018 at 03:22:01PM +0100, William McCaffery wrote:
> That sounds reasonable, especially if we want to keep them as discreet
> projects. If Andreas would be willing to set this up that would be great.

Please have a look at

    https://salsa.debian.org/blends-team/biolinux

To have some content I have choosen a copy of med-bio for biolinux-desktop
and med-bio-dev for biolinux-server which is definitely *not* sensible, but
works as a test case.  Please adapt the tasks (including the Description in
the top) to your preference.  Once you have something reasonable I'll setup
the websentinel config to have tasks pages for BioLinux.
 
> As far as I can tell from the Debian documentation and what we've discussed,
> the complete set of Bio-Linux tasks would simply be Tim's original package
> list, divided into desktop and server tasks. I would ask your preference on
> whether we would use the reduced list I created which only has packages in
> sid (although this has some issues with virtual packages) or the compete
> set. I know that the documentation states the latter, but I don't know if
> all of the packages are still useful to Bio-Linux. As  for separating
> Bio-Linux server and client packages, I can go through Tim's packages and
> try and create a list of packages for a server task for review.

Please check all files for spelling issues etc.  There is no point in
manually editing debian/control or biolinux-tasks.desc since these are
autogenerated.  You get them by

     make dist

Hope this helps over the first hurdle but keep on asking here.  I'll be
more responsive soon (just in the train back home from DebConf).

Thanks for the effort to merge BioLinux and Debian Med - I'm positive
about a great and productive cooperation

     Andreas.

--
http://fam-tille.de

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Re: Bio-Linux

Tony Travis
On 06/08/18 11:12, Andreas Tille wrote:

> Hi William and Tony,
>
> On Fri, Aug 03, 2018 at 03:22:01PM +0100, William McCaffery wrote:
>> That sounds reasonable, especially if we want to keep them as discreet
>> projects. If Andreas would be willing to set this up that would be great.
>
> Please have a look at
>
>     https://salsa.debian.org/blends-team/biolinux
>
> To have some content I have choosen a copy of med-bio for biolinux-desktop
> and med-bio-dev for biolinux-server which is definitely *not* sensible, but
> works as a test case.  Please adapt the tasks (including the Description in
> the top) to your preference.  Once you have something reasonable I'll setup
> the websentinel config to have tasks pages for BioLinux.

Hi, Andreas.

I've just had a look, but I see all packages set as 'Recommends' - How
do I configure them to be installed?

>> As far as I can tell from the Debian documentation and what we've discussed,
>> the complete set of Bio-Linux tasks would simply be Tim's original package
>> list, divided into desktop and server tasks. I would ask your preference on
>> whether we would use the reduced list I created which only has packages in
>> sid (although this has some issues with virtual packages) or the compete
>> set. I know that the documentation states the latter, but I don't know if
>> all of the packages are still useful to Bio-Linux. As  for separating
>> Bio-Linux server and client packages, I can go through Tim's packages and
>> try and create a list of packages for a server task for review.

The main packages in the server metapackage are the Apache web server
and Galaxy, plus the x2go server. Neither of these are useful on a
'live' USB/DVD or minimal install on a low-spec PC.

> Please check all files for spelling issues etc.  There is no point in
> manually editing debian/control or biolinux-tasks.desc since these are
> autogenerated.  You get them by
>
>      make dist
>
> Hope this helps over the first hurdle but keep on asking here.  I'll be
> more responsive soon (just in the train back home from DebConf).

It helps a LOT!

> Thanks for the effort to merge BioLinux and Debian Med - I'm positive
> about a great and productive cooperation

Me too :-)

  Tony.

--
Minke Informatics Limited, Registered in Scotland - Company No. SC419028
Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK)
tel. +44(0)19755 63548                    http://minke-informatics.co.uk
mob. +44(0)7985 078324        mailto:[hidden email]

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Re: Bio-Linux

Andreas Tille-5
Hi Tony,

On Mon, Aug 06, 2018 at 11:48:58AM +0200, Tony Travis wrote:

> > Please have a look at
> >
> >     https://salsa.debian.org/blends-team/biolinux
> >
> > To have some content I have choosen a copy of med-bio for biolinux-desktop
> > and med-bio-dev for biolinux-server which is definitely *not* sensible, but
> > works as a test case.  Please adapt the tasks (including the Description in
> > the top) to your preference.  Once you have something reasonable I'll setup
> > the websentinel config to have tasks pages for BioLinux.
>
> I've just had a look, but I see all packages set as 'Recommends' - How
> do I configure them to be installed?

Recommends are installed on default installations.  You need to force
apt by --no-install-recommends in case you want to stop apt from doing
this and this is how metapackages should work.  You once installed

    apt-get install med-bio

and got all the Recommends, right?
 
> The main packages in the server metapackage are the Apache web server
> and Galaxy, plus the x2go server. Neither of these are useful on a
> 'live' USB/DVD or minimal install on a low-spec PC.

Just add these packages to the server package (and for sure remove what
needs to be removed.  It seems there is some packaging work left for
galaxy server).
 

> > Please check all files for spelling issues etc.  There is no point in
> > manually editing debian/control or biolinux-tasks.desc since these are
> > autogenerated.  You get them by
> >
> >      make dist
> >
> > Hope this helps over the first hurdle but keep on asking here.  I'll be
> > more responsive soon (just in the train back home from DebConf).
>
> It helps a LOT!

:-)
 
> > Thanks for the effort to merge BioLinux and Debian Med - I'm positive
> > about a great and productive cooperation
>
> Me too :-)

Happy to contribute to BioLinux

      Andreas.

--
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Re: Bio-Linux

William-9
In reply to this post by Andreas Tille-5
Hi Andreas, thanks for setting that up,  like Tony said it helps a lot. I'll get on setting up the tasks.

Thanks again,

William



On Mon, 6 Aug 2018, 10:12 Andreas Tille, <[hidden email]> wrote:
Hi William and Tony,

On Fri, Aug 03, 2018 at 03:22:01PM +0100, William McCaffery wrote:
> That sounds reasonable, especially if we want to keep them as discreet
> projects. If Andreas would be willing to set this up that would be great.

Please have a look at

    https://salsa.debian.org/blends-team/biolinux

To have some content I have choosen a copy of med-bio for biolinux-desktop
and med-bio-dev for biolinux-server which is definitely *not* sensible, but
works as a test case.  Please adapt the tasks (including the Description in
the top) to your preference.  Once you have something reasonable I'll setup
the websentinel config to have tasks pages for BioLinux.

> As far as I can tell from the Debian documentation and what we've discussed,
> the complete set of Bio-Linux tasks would simply be Tim's original package
> list, divided into desktop and server tasks. I would ask your preference on
> whether we would use the reduced list I created which only has packages in
> sid (although this has some issues with virtual packages) or the compete
> set. I know that the documentation states the latter, but I don't know if
> all of the packages are still useful to Bio-Linux. As  for separating
> Bio-Linux server and client packages, I can go through Tim's packages and
> try and create a list of packages for a server task for review.

Please check all files for spelling issues etc.  There is no point in
manually editing debian/control or biolinux-tasks.desc since these are
autogenerated.  You get them by

     make dist

Hope this helps over the first hurdle but keep on asking here.  I'll be
more responsive soon (just in the train back home from DebConf).

Thanks for the effort to merge BioLinux and Debian Med - I'm positive
about a great and productive cooperation

     Andreas.

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Re: Bio-Linux

Steffen Möller
In reply to this post by Andreas Tille-5
Hi Andreas, hi Tony,

On 8/6/18 11:12 AM, Andreas Tille wrote:

> Hi William and Tony,
>
> On Fri, Aug 03, 2018 at 03:22:01PM +0100, William McCaffery wrote:
>> That sounds reasonable, especially if we want to keep them as discreet
>> projects. If Andreas would be willing to set this up that would be great.
> Please have a look at
>
>     https://salsa.debian.org/blends-team/biolinux
>
> To have some content I have choosen a copy of med-bio for biolinux-desktop
> and med-bio-dev for biolinux-server which is definitely *not* sensible, but
> works as a test case.  Please adapt the tasks (including the Description in
> the top) to your preference.  Once you have something reasonable I'll setup
> the websentinel config to have tasks pages for BioLinux.

from my side I would be particularly interested to learn about the
packages that Bio-Linux wants to see redistributed with them but that
are yet not in Debian.

The https://blends.debian.org/med/tasks/bio pages have that yellow
section that lists a few bio-linux ones. How would you (Andreas and
Tony) feel about moving them to the Bio-Linux list?

>  
>> As far as I can tell from the Debian documentation and what we've discussed,
>> the complete set of Bio-Linux tasks would simply be Tim's original package
>> list, divided into desktop and server tasks. I would ask your preference on
>> whether we would use the reduced list I created which only has packages in
>> sid (although this has some issues with virtual packages) or the compete
>> set.
The complete list, I propose. The colouring to indicate what is
available and what is on salsa etc is done in an automated fashion.
>> I know that the documentation states the latter, but I don't know if
>> all of the packages are still useful to Bio-Linux.
I tend to agree that a refurbished Bio-Linux should address today's
problems more than the ones of the past. But you can easily remove
packages by just deleting a line, so, first let's have a look about how
much we already cover.

>> As  for separating
>> Bio-Linux server and client packages, I can go through Tim's packages and
>> try and create a list of packages for a server task for review.
> Please check all files for spelling issues etc.  There is no point in
> manually editing debian/control or biolinux-tasks.desc since these are
> autogenerated.  You get them by
>
>      make dist
>
> Hope this helps over the first hurdle but keep on asking here.  I'll be
> more responsive soon (just in the train back home from DebConf).
>
> Thanks for the effort to merge BioLinux and Debian Med - I'm positive
> about a great and productive cooperation

Ok.  I am not sure about how far we are from everything. It would help
if we just have something as a start.

Best,

Steffen


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Re: Bio-Linux

Andreas Tille-5
Hi Steffen,

On Wed, Aug 15, 2018 at 05:40:51PM +0200, Steffen Möller wrote:

> >
> >     https://salsa.debian.org/blends-team/biolinux
> >
> > To have some content I have choosen a copy of med-bio for biolinux-desktop
> > and med-bio-dev for biolinux-server which is definitely *not* sensible, but
> > works as a test case.  Please adapt the tasks (including the Description in
> > the top) to your preference.  Once you have something reasonable I'll setup
> > the websentinel config to have tasks pages for BioLinux.
>
> from my side I would be particularly interested to learn about the
> packages that Bio-Linux wants to see redistributed with them but that
> are yet not in Debian.

We actually have this kind of documentation since our latest sprint.
Unfortunately it seems to be in a simila maintenance situation that
overworked contributors do not find the time to care for it.  I now
finally removed what I once marked as "in Debian" - please double check
my latest commit:

    https://salsa.debian.org/med-team/community/bio-linux/commit/090871600b1f72a532a449d88af9f118b0d95868

It would be a really helpful contribution from BioLinux if you could
maintain this list to point package maintainers to the **urgently**
**needed** software to start with this to spent our time in a sensible
manner.  I'm also offering mentoring to learn how to properly package
inside the Debian Med team[1].
 
> The https://blends.debian.org/med/tasks/bio pages have that yellow
> section that lists a few bio-linux ones. How would you (Andreas and
> Tony) feel about moving them to the Bio-Linux list?

You mean to the the according task file?  Its currently in the desktop
task since its a stupic copy of or bio task.  I did not yet activated
the web rendering since I understood Bio-Linux developers wanted to
create something more sensible first.  Please let me know if you need
further help to accomplish this.  If you do not ask questions I have
no idea how to help.

> >> As far as I can tell from the Debian documentation and what we've discussed,
> >> the complete set of Bio-Linux tasks would simply be Tim's original package
> >> list, divided into desktop and server tasks. I would ask your preference on
> >> whether we would use the reduced list I created which only has packages in
> >> sid (although this has some issues with virtual packages)

What are the issues with virtual packages?

> >> or the compete set.
> The complete list, I propose. The colouring to indicate what is
> available and what is on salsa etc is done in an automated fashion.

I'd also vote to keep the long list and show what is missing / what
we are working on.  The Blends toolset is dealing sensibly with the
missings when it will create the metapackages.

> >> I know that the documentation states the latter, but I don't know if
> >> all of the packages are still useful to Bio-Linux.
> I tend to agree that a refurbished Bio-Linux should address today's
> problems more than the ones of the past. But you can easily remove
> packages by just deleting a line, so, first let's have a look about how
> much we already cover.

I agree with Steffen that removals are very cheap to do.  If I were you
I would start with a sensible long list and reduce later in a second
rush.

> > Hope this helps over the first hurdle but keep on asking here.  I'll be
> > more responsive soon (just in the train back home from DebConf).
> >
> > Thanks for the effort to merge BioLinux and Debian Med - I'm positive
> > about a great and productive cooperation
>
> Ok.  I am not sure about how far we are from everything. It would help
> if we just have something as a start.

+1

Kind regards

      Andreas.
 

[1] https://wiki.debian.org/DebianMed/MoM

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Re: Bio-Linux

Tony Travis
On 16/08/18 08:24, Andreas Tille wrote:

> [...]
> It would be a really helpful contribution from BioLinux if you could
> maintain this list to point package maintainers to the **urgently**
> **needed** software to start with this to spent our time in a sensible
> manner.  I'm also offering mentoring to learn how to properly package
> inside the Debian Med team[1].
>  
>> The https://blends.debian.org/med/tasks/bio pages have that yellow
>> section that lists a few bio-linux ones. How would you (Andreas and
>> Tony) feel about moving them to the Bio-Linux list?

Hi, Steffen and Andreas.

Good idea - I'll do that, but I'm on holiday just now driving through
France and only have intermittent access to the Internet. I'll do what I
can when I can. I won't be back home again until 2 Oct, but Will might
be able to sort it out for me.

Thanks,

  Tony.

--
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Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK)
tel. +44(0)19755 63548                    http://minke-informatics.co.uk
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Re: Bio-Linux

Andreas Tille-5
On Thu, Aug 16, 2018 at 12:47:21PM +0200, Tony Travis wrote:

> >  
> >> The https://blends.debian.org/med/tasks/bio pages have that yellow
> >> section that lists a few bio-linux ones. How would you (Andreas and
> >> Tony) feel about moving them to the Bio-Linux list?
>
> Hi, Steffen and Andreas.
>
> Good idea - I'll do that, but I'm on holiday just now driving through
> France and only have intermittent access to the Internet. I'll do what I
> can when I can. I won't be back home again until 2 Oct, but Will might
> be able to sort it out for me.

Enjoy your holiday!  But please don't make me jealous by confirming
that these holidays will last until beginning of October. ;-)

Kind regards

       Andreas.

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Re: Bio-Linux

Tony Travis
On 16/08/18 13:39, Andreas Tille wrote:

> On Thu, Aug 16, 2018 at 12:47:21PM +0200, Tony Travis wrote:
>>>  
>>>> The https://blends.debian.org/med/tasks/bio pages have that yellow
>>>> section that lists a few bio-linux ones. How would you (Andreas and
>>>> Tony) feel about moving them to the Bio-Linux list?
>>
>> Hi, Steffen and Andreas.
>>
>> Good idea - I'll do that, but I'm on holiday just now driving through
>> France and only have intermittent access to the Internet. I'll do what I
>> can when I can. I won't be back home again until 2 Oct, but Will might
>> be able to sort it out for me.
>
> Enjoy your holiday!  But please don't make me jealous by confirming
> that these holidays will last until beginning of October. ;-)

Hi, Andreas.

Not quite, I'm returning to the Mario Negri Institute in Milan to work
there for two weeks on 17 Sep, then back to work at the University of
Aberdeen on 2 Oct. I'll try to make some progress on the list by then.

Just four weeks holiday :-)

Bye,

  Tony.

--
Minke Informatics Limited, Registered in Scotland - Company No. SC419028
Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK)
tel. +44(0)19755 63548                    http://minke-informatics.co.uk
mob. +44(0)7985 078324        mailto:[hidden email]

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Re: Bio-Linux

Steffen Möller
In reply to this post by Tony Travis
Hello Tony,

On 8/16/18 12:47 PM, Tony Travis wrote:

> On 16/08/18 08:24, Andreas Tille wrote:
>> [...]
>> It would be a really helpful contribution from BioLinux if you could
>> maintain this list to point package maintainers to the **urgently**
>> **needed** software to start with this to spent our time in a sensible
>> manner.  I'm also offering mentoring to learn how to properly package
>> inside the Debian Med team[1].
>>  
>>> The https://blends.debian.org/med/tasks/bio pages have that yellow
>>> section that lists a few bio-linux ones. How would you (Andreas and
>>> Tony) feel about moving them to the Bio-Linux list?
> [...]
>
> Good idea - I'll do that, but I'm on holiday just now driving through
> France and only have intermittent access to the Internet. I'll do what I
> can when I can. I won't be back home again until 2 Oct, but Will might
> be able to sort it out for me.

By all means, enjoy your vacation.

I just uploaded OmegaMap as one of those Bio-Linux packages.

Cheers,

Steffen