From tbooth at ceh.ac.uk  Tue May 19 11:48:51 2015
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Tue, 19 May 2015 16:48:51 +0100
Subject: [Bio-linux-dev] Getting involved
In-Reply-To: <CALenahko-SW=57VBxHD-X7A52ojWU1rfd1dWB3hnwFNT61KwDQ@mail.gmail.com>
References: <55520561.2050009@calmblue.net>
 <1431442974.16741.13.camel@wllt1771.nerc-wallingford.ac.uk>
 <55535923.2020903@calmblue.net> <55535C30.2010604@minke-informatics.co.uk>
 <55535E8D.2070402@calmblue.net>
 <CALenahko-SW=57VBxHD-X7A52ojWU1rfd1dWB3hnwFNT61KwDQ@mail.gmail.com>
Message-ID: <1432050531.26429.12.camel@wllt1771.nerc-wallingford.ac.uk>

Hi,

In reply to a query on the users list from Raony Guimaraes, here is what
I would say to anyone wanting to get involved in Bio-Linux.

Raony Guimaraes Corr?a Do Carmo Lisboa Cardenas wrote:
> I believe I could help this project by packaging some new software to
> add to the biolinux repositories or even trying to upgrade a package 
> from python2 to python3.

The real community effort that keeps Bio-Linux going is Debian Med:

https://wiki.debian.org/DebianMed

So if you are not familiar with what these guys do and how they work
please take a little time to look at the their Wiki and recent mailing
list discussion.  It may sound counter-intuitive, but my ultimate goal is
to make Bio-Linux redundant by adding all the tools from Bio-Linux right
into Debian (and thus Ubuntu).  I don't necessarily expect to actually
achieve this, but it's where I'm heading!

If you are interested in packaging software then you should start by
signing up here and looking at the open tasks, or else announcing your
own interests on the list.  I'm happy to help with packaging questions
myself but I'm easily distracted as I have a lot on.  If you post to the
Debian-Med lists you are likely to get answers much more quickly than if
you rely on me.

I can pull any packages from Deb-Med GIT or SVN into Bio-Linux in just a
few minutes.  No need to wait for a new Bio-Linux release.

On the specific question of converting Python2 to Python3, that's really
a call for the developers of the software.  When I add tools to
Bio-Linux I try to modify them as little as possible - usually just
enough to work with the other packages on the system.  Some developers
can be very possessive of their code; others will welcome help with open
arms.  You just have to ask.

Cheers,

TIM

-- 
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 

Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB 

http://environmentalomics.org/bio-linux
+44 1491 69 2297


-- 
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 

Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB 

http://environmentalomics.org/bio-linux
+44 1491 69 2297



From raonyguimaraes at gmail.com  Tue May 19 14:00:58 2015
From: raonyguimaraes at gmail.com (=?ISO-8859-1?Q?Raony_Guimaraes_Corr=EAa_Do_Carmo_Lisboa_Cardenas?=)
Date: Tue, 19 May 2015 15:00:58 -0300
Subject: [Bio-linux-dev] Getting involved
In-Reply-To: <1432050531.26429.12.camel@wllt1771.nerc-wallingford.ac.uk>
References: <55520561.2050009@calmblue.net>
 <1431442974.16741.13.camel@wllt1771.nerc-wallingford.ac.uk>
 <55535923.2020903@calmblue.net> <55535C30.2010604@minke-informatics.co.uk>
 <55535E8D.2070402@calmblue.net>
 <CALenahko-SW=57VBxHD-X7A52ojWU1rfd1dWB3hnwFNT61KwDQ@mail.gmail.com>
 <1432050531.26429.12.camel@wllt1771.nerc-wallingford.ac.uk>
Message-ID: <CALenah=M3FgdgKqwPgMJCzhJ_J=QPG9ogKSJE=AnwnkwdfOQ7w@mail.gmail.com>

Hi Tim,

I agree with you that Debian Med should be the main focus for new packaging
contribution. I've been following the discussions in both projects for some
time already.

Thank you for your message :)



_____________________________________________

Raony Guimar?es Corr?a Do Carmo Lisboa Cardenas
PhD Student in Bioinformatics

email: raonyguimaraes at gmail.com
skype/gtalk: raonyguimaraes
phone: +55 31 93404152

Laboratory of Clinical Genomics
UFMG School of Medicine
Federal University of Minas Gerais - UFMG
Av. Prof. Alfredo Balena, 190, Sala 321
Belo Horizonte, Brazil 30130-100
_____________________________________________

On Tue, May 19, 2015 at 12:48 PM, Tim Booth <tbooth at ceh.ac.uk> wrote:

> Hi,
>
> In reply to a query on the users list from Raony Guimaraes, here is what
> I would say to anyone wanting to get involved in Bio-Linux.
>
> Raony Guimaraes Corr?a Do Carmo Lisboa Cardenas wrote:
> > I believe I could help this project by packaging some new software to
> > add to the biolinux repositories or even trying to upgrade a package
> > from python2 to python3.
>
> The real community effort that keeps Bio-Linux going is Debian Med:
>
> https://wiki.debian.org/DebianMed
>
> So if you are not familiar with what these guys do and how they work
> please take a little time to look at the their Wiki and recent mailing
> list discussion.  It may sound counter-intuitive, but my ultimate goal is
> to make Bio-Linux redundant by adding all the tools from Bio-Linux right
> into Debian (and thus Ubuntu).  I don't necessarily expect to actually
> achieve this, but it's where I'm heading!
>
> If you are interested in packaging software then you should start by
> signing up here and looking at the open tasks, or else announcing your
> own interests on the list.  I'm happy to help with packaging questions
> myself but I'm easily distracted as I have a lot on.  If you post to the
> Debian-Med lists you are likely to get answers much more quickly than if
> you rely on me.
>
> I can pull any packages from Deb-Med GIT or SVN into Bio-Linux in just a
> few minutes.  No need to wait for a new Bio-Linux release.
>
> On the specific question of converting Python2 to Python3, that's really
> a call for the developers of the software.  When I add tools to
> Bio-Linux I try to modify them as little as possible - usually just
> enough to work with the other packages on the system.  Some developers
> can be very possessive of their code; others will welcome help with open
> arms.  You just have to ask.
>
> Cheers,
>
> TIM
>
> --
> Tim Booth <tbooth at ceh.ac.uk>
> NERC Environmental Bioinformatics Centre
>
> Centre for Ecology and Hydrology
> Maclean Bldg, Benson Lane
> Crowmarsh Gifford
> Wallingford, England
> OX10 8BB
>
> http://environmentalomics.org/bio-linux
> +44 1491 69 2297
>
>
> --
> Tim Booth <tbooth at ceh.ac.uk>
> NERC Environmental Bioinformatics Centre
>
> Centre for Ecology and Hydrology
> Maclean Bldg, Benson Lane
> Crowmarsh Gifford
> Wallingford, England
> OX10 8BB
>
> http://environmentalomics.org/bio-linux
> +44 1491 69 2297
>
>
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