Re: Debian Med Bioinformatics Sprint in Lübeck : post-install
On Wed, Feb 02, 2011 at 06:19:57PM +0000, Tim Booth wrote:
> I generally have an aversion to mailing list servers that create a
> public mail archive with e-mail addresses unobfuscated, but as I see the
> damage is now done and my address is on there for all to spam I may as
> well join.
Ahh, hmm, I see. I seem to be routine-blinded because using so many
public lists (and using heavy spam filtering). Sorry if I tapped hereby
on somebodies shoes - turning the recievers into BCC would have helped
here. My fault. :-(
> The page at the moment rather assumes that you already know how to package.
It seems our documentation makes some more of this kind of false
assumptions ...
> It also
> outlines a development process using SVN-buildpackage that nobody
> actually seems to follow in real life.
May be that is a bit to strong. I *personally* do not like
svn-buildpackage and I have heard rumors that people had trouble setting
it up. I also have heard that people had more success with
git-buildpackage and there seems to be a tendency that people are moving
from SVN to Git if you look at the big picture (not specifically at the
Debian Med project). (I just noticed that when working on the packaging
in the train it would have had advantages to use git because it would
have enabled me to make more fine grained commits - but that's a rare
case.)
In general those tools are designed to make your live easy. There is
actually no need to use the tools as long as you provide policy conform
packages. If you prefer to do manually what the tool can do for you in
principle that's perfectly fine. People who finally included those
tools in their own workflow and adapted to using it have learned about
their advantages over doing things manually and try to propagate this
knowledge to simplify the life of beginners but to some extend newcomers
have a limited capacity to learn all the new things and need to adapt
slowly. That's fine.
> Also the page needs to say something to non-developers who come looking
> for software. It's not immediately clear to a newcomer what exactly
> Debian Med is doing and why there are no direct package downloads on the
> site.
I'm keen on hearing what you or the other newcomers would have expected
to read to get a better understanding. The fact that there is nothing
to download can be easily explained: It's just Debian and you do not
download but apt-get install. What would you consider a proper place to
explain this?
> (The phrase "Pure Blend" does not mean much to the average user).
> Maybe a short FAQ is appropriate?
http://wiki.debian.org/DebianPureBlends ?
> During the meeting I was editing the T-Coffee package on my laptop as I
> had a head start over Paolo in terms of software setup and understanding
> of package building tools. Our main achievement was to review and
> update all dependencies (T-Coffee has many). TMalign
TMalign will be in new at the end of this week (if nothing unexpected
will happen.
> along with BLAST+
> enables a key mode of operation in T-Coffee but currently the BLAST+ bit
> only works with our bio-linux-blast+ package. I'm continuing to work on
> this.
Did you actually found out what BLAST+ is (I remember you were wondering
about the difference between blast2 and blast+).
> Apart from that we compiled the latest upstream (only on Ubuntu Lucid -
> someone needs to try it on Sid!) and also did a bit of tidying with help
> from Andreas.
Just tell us were the stuff we should test is located (simply commit the
packaging stuff to SVN).
> Paolo should still be the maintainer of this package from now on, unless
> we scared him off ;-) As I now have a lot more confidence about my
> understanding of packaging I'll try to help and encourage him (and
> others) on the list.
I'm fine with giving Paolo any helping hand he might need.
> Excellent news on Mothur after it sat in the SVN for so long due to
> license ambiguity. This is a very important package to me so maybe a
> logical one for me to take on as maintainer once it goes in?
Just add yourself to the uploaders field, work on the packaging in SVN
and ask on the list that somebody of the DDs should upload.
Kind regards
Andreas.
--
http://fam-tille.de
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