Re: ensembl_57-7_amd64.changes ACCEPTED into experimental
Hi George,
thanks for the verbose introduction.
On Fri, Apr 01, 2011 at 07:52:49PM +0300, George Marselis wrote:
> While it is true that I
> cannot put a (good) package together, yet, I can definitely recite all
> the O'Reilly books by heart.
This proves that there is an evident need for an O'Reilly book about
Debian packaging. :-)
> Sorry, no Java. Just C, Perl, Python, LISP, bit of Erlang, .NET and
> (shamed to admit it) PHP. Any packages in LISP?
There is no need to be ashamed of. IMHO you can write good and bad
software in any language - so no need for language bashing ...
If you are asking for packages in LISP our tasks files only have one
hit which is Prism:
http://debian-med.alioth.debian.org/tasks/oncology#prism
The language a project is written in is actually not rendered at these
web pages but I just greped
svn://svn.debian.org/svn/blends/projects/med/trunk/debian-med/tasks
and got this. There is a good chance that other projects are written
in LISP as well but the info is not recorded in our tasks files.
> I work for the Computational Biosciences Research Center in King
> Abdullal University of Science and Technology (KAUST), a brand new
> graduate research university, which His Majesty King Abdullal,
> envisioned for Saudi Arabia back in the 80s. There are several EBI,
> NCBI and Sanger people over here. We got a good crew and we hop to
> rock the bioinformatics world in the years to come.
IMHO it is a very good idea to package what is needed at your institute
but not yet packaged in Debian. Please have a close look into the
Debian Med policy document[1] to learn what is needed to join the Debian
Med team (alioth account) and where to commit your packaging for optimal
cooperation. We have some success story to turn interested people with
limited packaging skills into valuable team members with interesting
packages.
> In the meantime, I have to run a department where users ask for N+1
> bioinformatics tools. I am getting more familiar with those tools
> every day; less surprises every time I install them. So far we have
> used 75% of the cycles of the local supercomputer, using mpiblast, for
> the past year and a half. I had enough, though, trying to compile
> tools by hand all the time, and I want a way to just apt-get any tool
> my Researchers find on the web and catches their fancy (so I can slack
> off more, instead of compiling tools). Perfect case in hand is
> ensembl-hive which I have been banging my head against ever since Wed
> afternoon.
So IMHO your situation is the perfect position to join Debian Med.
> I thought I would start packaging by doing MIRA, since I was
> exchanging emails a lot with Bastien back in September. Right now,
> besides trying to fix a flood in my apartment, I am trying to hold our
> infrastructure together using gum and a string, while waiting for the
> grant money to build The Real Thing[tm]. I was on #debian-mentors for
> two months, but nobody was um, interested enough, to help me with my
> questions, so I kinda gave up. Two weeks ago, I picked up my interest
> again, only to have the NFS server of the cluster sing me "good night,
> sweet prince".
Some members of Debian Med are lurking on debian-mentors mailing list
but we are a bit IRC ignorant. So even if there exists a #debian-med
channel it is basically unused.
> Packaging for Debian is something I am really interested in; it will
> help me leverage my time by a thousand. I read the beginners book to
> packaging, but it could not see how I could apply that to mira. for
> example, Bastien lists Perl as a per-requisite. Do I include that in
> the package requirements? Stuff like that... If I could get a mentor
> to help me over the initial hump, I would def be of use around here
> (but no learning Java, please).
You might like to check out
svn://svn.debian.org/svn/debian-med/trunk/packages/mira/trunk/
(preferably after you became a member of Debian Med on Alioth and use
svn+ssh to commit your changes). The actual question is answered there
as
Build-Depends: ..., perl
If you have more questions feel free to ask here!
Kind regards
Andreas.
[1] http://debian-med.alioth.debian.org/docs/policy.html
--
http://fam-tille.de
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