Re: Participating in Debian Med for GSoC

2016-03-14 Thread Andreas Tille 
Hi Jihyeok,
 
On Tue, Mar 15, 2016 at 01:13:53AM +0900, Jihyeok Seo wrote:
> 
> Thought I’d introduce myself to the list by forwarding this email. Thank you 
> for the kind instructions, Andreas!

Thankls for your interest in Debian Med and showing up here.
 
> I’m a huge fan of testing and verifying software correctness, so I’m very 
> excited about working on the Debian Med CI project, regardless of GSoC.

That's fine for sure.  I think we can need any helping hand to increase
testing.
 
> I signed up on Alioth as limeburst(-guest?),

Added to Debian Med project which grants you commit permission.

> and I’m open to suggestions as to which packages I should start contributing 
> to.

Feel free to pick one yourself.  Anna intended to start with bwa so we
should not touch this in the moment.  You might like to check prodigal
where I have given hints here:

   https://lists.debian.org/debian-med/2016/02/msg00123.html

May be it makes sense to create a Wiki page

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

(or what better name you might invent) where Anna and you specify their
near time targets and tick-mark if the target is done.

Kind regards

   Andreas.

> Regards,
> Jihyeok
> 
> > On Mar 9, 2016, at 12:38 AM, Andreas Tille  wrote:
> > 
> > Hi Jihyeok,
> > 
> > thanks for your interest in the CI project.
> > 
> > On Tue, Mar 08, 2016 at 03:53:12PM +0900, Jihyeok Seo wrote:
> >> My name is Jihyeok Seo, and I am a student studying biology and computer 
> >> science at Konkuk University.
> > 
> > The combination of biology and computer science is exactly the
> > qualification that is needed for the project.
> > 
> >> I’ve been thinking about writing a proposal for this year’s Google Summer 
> >> of Code, and the CI project[1] listed on the Debian GSoC wiki caught my 
> >> interest. I’m curious whether there are small tasks related to this 
> >> project I can work on before writing my proposal.
> > 
> > If you read this thread on the Debian Med mailing list
> > 
> >   https://lists.debian.org/debian-med/2016/02/msg00116.html
> > 
> > you should get some idea about small tasks.  Please also read the Debian
> > Med policy[4] to learn about the technique used in the team.  The first
> > parts of the thread above should help you getting an alioth login.
> > 
> > Once you are able to login there please show up on the mailing list and
> > we can coordinate tasks there.
> > 
> >> I don’t have much programming experience, but I’ll leave a link to my 
> >> GitHub profile[2]. I have worked with PDB(Protein Data Bank) files, 
> >> validating and correcting errors. I also wrote some test cases for a FASTA 
> >> parser in my advisor’s lab. I have some experience writing tests and CI 
> >> from when I was contributing to the Earth Reader[3] project, and others.
> > 
> > I think some basic shell scripting is sufficient for the job - the more
> > important thing is that you know the biologic applications and you are
> > able to evaluate the results.
> > 
> >> I have subscribed to the debian-med mailing list, and now going through 
> >> the Med wiki. You can contact me by this email address, or I’m limeburst 
> >> on OFTC. Thank you for your guidance!
> > 
> > Nice to know that you are subscribed.  If needed we could also meet on
> > IRC but in general I prefer public discussion on the list.  So even feel
> > free to quote me in public there when responding to this mail.
> > 
> > Kind regards
> > 
> >  Andreas.
> > 
> >> Jihyeok
> >> 
> >> [1]: 
> >> https://wiki.debian.org/SummerOfCode2016/Projects#SummerOfCode2016.2FProjects.2FBioToolsTesting.Continuous_Integration_for_all_biological_applications_inside_Debian
> >> [2]: https://github.com/limeburst
> >> [3]: http://earthreader.org
> > 
> > [4] http://debian-med.alioth.debian.org/docs/policy.html
> > 
> > -- 
> > http://fam-tille.de
> > 
> > 
> > 
> 
> 

-- 
http://fam-tille.de

Re: how to get list of debianmed packages

2016-03-14 Thread Andreas Tille 
On Mon, Mar 14, 2016 at 05:15:50PM +0100, Olivier Sallou wrote:
> > May be we should bundle better tools inside metapackages to output
> > the dependencies of the package in a nice way ...
> a web interface with json (or equivalent) search/output would be nice
> too to get programmatic search by tools. (even not from a Debian box).

OK, we have a web interface:

   http://blends.debian.org/med/tasks/bio

We could also generate

   http://blends.debian.org/med/tasks/bio.json

if you specify *what exactly* should be included.

Kind regards

   Andreas. 

-- 
http://fam-tille.de

Re: how to get list of debianmed packages

2016-03-14 Thread Olivier Sallou 


On 03/14/2016 05:04 PM, Andreas Tille wrote:
> On Mon, Mar 14, 2016 at 04:38:08PM +0100, Olivier Sallou wrote:
>> how can I get a programmatic list of debianmed packages, possibly by
>> section (bioinformatics ,...) ?
> grep-aptavail --field=Maintainer 
> 'debian-med-packag...@lists.alioth.debian.org' 
> --show-field=Package,Version,Description
>
> May be we should bundle better tools inside metapackages to output
> the dependencies of the package in a nice way ...
a web interface with json (or equivalent) search/output would be nice
too to get programmatic search by tools. (even not from a Debian box).
>
> Kind regards
>
> Andreas.
>
>

-- 
Olivier Sallou
IRISA / University of Rennes 1
Campus de Beaulieu, 35000 RENNES - FRANCE
Tel: 02.99.84.71.95

gpg key id: 4096R/326D8438  (keyring.debian.org)
Key fingerprint = 5FB4 6F83 D3B9 5204 6335  D26D 78DC 68DB 326D 8438

Re: Participating in Debian Med for GSoC

2016-03-14 Thread Jihyeok Seo 
Hello!

Thought I’d introduce myself to the list by forwarding this email. Thank you 
for the kind instructions, Andreas!

I’m a huge fan of testing and verifying software correctness, so I’m very 
excited about working on the Debian Med CI project, regardless of GSoC.

I signed up on Alioth as limeburst(-guest?), and I’m open to suggestions as to 
which packages I should start contributing to.

Regards,
Jihyeok

> On Mar 9, 2016, at 12:38 AM, Andreas Tille  wrote:
> 
> Hi Jihyeok,
> 
> thanks for your interest in the CI project.
> 
> On Tue, Mar 08, 2016 at 03:53:12PM +0900, Jihyeok Seo wrote:
>> My name is Jihyeok Seo, and I am a student studying biology and computer 
>> science at Konkuk University.
> 
> The combination of biology and computer science is exactly the
> qualification that is needed for the project.
> 
>> I’ve been thinking about writing a proposal for this year’s Google Summer of 
>> Code, and the CI project[1] listed on the Debian GSoC wiki caught my 
>> interest. I’m curious whether there are small tasks related to this project 
>> I can work on before writing my proposal.
> 
> If you read this thread on the Debian Med mailing list
> 
>   https://lists.debian.org/debian-med/2016/02/msg00116.html
> 
> you should get some idea about small tasks.  Please also read the Debian
> Med policy[4] to learn about the technique used in the team.  The first
> parts of the thread above should help you getting an alioth login.
> 
> Once you are able to login there please show up on the mailing list and
> we can coordinate tasks there.
> 
>> I don’t have much programming experience, but I’ll leave a link to my GitHub 
>> profile[2]. I have worked with PDB(Protein Data Bank) files, validating and 
>> correcting errors. I also wrote some test cases for a FASTA parser in my 
>> advisor’s lab. I have some experience writing tests and CI from when I was 
>> contributing to the Earth Reader[3] project, and others.
> 
> I think some basic shell scripting is sufficient for the job - the more
> important thing is that you know the biologic applications and you are
> able to evaluate the results.
> 
>> I have subscribed to the debian-med mailing list, and now going through the 
>> Med wiki. You can contact me by this email address, or I’m limeburst on 
>> OFTC. Thank you for your guidance!
> 
> Nice to know that you are subscribed.  If needed we could also meet on
> IRC but in general I prefer public discussion on the list.  So even feel
> free to quote me in public there when responding to this mail.
> 
> Kind regards
> 
>  Andreas.
> 
>> Jihyeok
>> 
>> [1]: 
>> https://wiki.debian.org/SummerOfCode2016/Projects#SummerOfCode2016.2FProjects.2FBioToolsTesting.Continuous_Integration_for_all_biological_applications_inside_Debian
>> [2]: https://github.com/limeburst
>> [3]: http://earthreader.org
> 
> [4] http://debian-med.alioth.debian.org/docs/policy.html
> 
> -- 
> http://fam-tille.de
> 
> 
>

Re: how to get list of debianmed packages

2016-03-14 Thread Alex Mestiashvili 
Hi,

On 03/14/2016 04:38 PM, Olivier Sallou wrote:
> Hi,
> how can I get a programmatic list of debianmed packages, possibly by
> section (bioinformatics ,...) ?
> 
> Thanks
> 
> Olivier
> 

May be something like that ?

 aptitude search "?maintainer(debian-med-packag...@lists.alioth.debian.org)"

you can also customize the search, see

http://algebraicthunk.net/~dburrows/projects/aptitude/doc/en/ch02s03s05.html

Best,
Alex

how to get list of debianmed packages

2016-03-14 Thread Olivier Sallou 
Hi,
how can I get a programmatic list of debianmed packages, possibly by
section (bioinformatics ,...) ?

Thanks

Olivier

-- 
Olivier Sallou
IRISA / University of Rennes 1
Campus de Beaulieu, 35000 RENNES - FRANCE
Tel: 02.99.84.71.95

gpg key id: 4096R/326D8438  (keyring.debian.org)
Key fingerprint = 5FB4 6F83 D3B9 5204 6335  D26D 78DC 68DB 326D 8438