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Re: How to proceed

Hi Christoph,

On Thu, Oct 20, 2011 at 09:15:38PM +0200, Dr. med. Christoph Gille wrote:
> Thanks Olivier and Andreas, both, ssh and svn co
> svn+ssh://svn.debian.org/svn/debian-med/trunk work very well now. I
> can even commit changes.

:-)
I have noticed that you created trunk/packages/neobio/trunk/debian.
Looking foreward to see some content in this dir.  Just do not be afraid
about making mistakes - we will help correcting them.
 
> When I had a look at the other projects, I noticed, that I
> probably did everything wrong. )-:

Well, everything is a bit hard: At least you were looking at the other
projects - this is perfectly right. :-)

> For the Fortran program tm-align I followed
> http://wiki.debian.org/IntroDebianPackaging.  I created a source
> package using debuild -us -uc. The directory structure looked like the
> ones in the svn directory, but finally I realized that tm-align
> already existed. Someone is already working on it. )-: Nevertheless,
> it was a good training.

Before I start working on (any, not necessarily Debian Med related)
package I do an "apt-cache search <pkg>" which in this case shows:

$ apt-cache search tm-align
tm-align - structual alignment of proteins

I also can not recommend frequently enough to closely watch our tasks
page

    http://debian-med.alioth.debian.org/tasks/bio

which shows a (hopefully) complete overview about the packages we just
included and those we are working on.  Please, before anybody starts
working on a package, just look at this (or the other categories) pages.
 
> For the other programs I followed
> http://tldp.org/HOWTO/html_single/Debian-Binary-Package-Building-HOWTO/
> since being Java-programs they are architecture independent and
> do not need compilation.  Here I created the dot deb files with
> fakeroot dpkg-deb -b. Was it a mistake not creating a source
> package?

Yes.  Well, OK, at least now I understand from where so many people get
a wrong understanding of building Debian packages.  I was always
wondering where people get this information and now I know ...

As a rule of thumb: Never (I really mean NEVER) start with an upper case
DEBIAN directory.  We are not shouting - we are building Debian
packages, right?  The only way to the official Debian mirror leads via
creating source packages and it is described in the "Debian New
Maintainers' Guide"[1].  (I personally wished that those other docs
would vanish from the web - ar at least would be ranked at rank >= 100.)
 
> My directories look different to those on the svn server because
> it is not a source package.  For example I wrote DEBIAN/control
> files but no debian/rules files.

General rule: These two features (DEBIAN/* and no debian/rules) are
a clear sign that you did packaging wrong (not everything - you just
asked here and this is right :-)).
 
> THE QUESTION:
> 
> Do I need to change all java based packages and
> create source packagess

Yes.

> in the same style as
> /srv/home/groups/pkg-escience/htdocs/debian/?

I see no reason to follow specifically pkg-escience rather than any
other repository, but in principle yes.  I usually copy-n-paste from
other projects inside the Debian Med repository.  So if I would start
packaging a Java package at first I would checkout the complete
Debian Med SVN and then I would grep for similar packages like this:

  $ grep -l "Depends:.*java" trunk/packages/*/trunk/debian/control

Currently you get 26 examples which are listing java in the Dependency
list (note: there are probably more because my quick shot does not
regard potential line breaks before the first java dependency).  Just
look at these and find something which looks similar to your program
in question.

> SECOND QUESTION:
> 
> On alioth in /srv/home/groups/pkg-escience/htdocs/debian I find dot
> deb files for example for biojava. How did these files get there?

In general: pkg-escience was as far as I can tell a small experiment for
only a view packages.  Do not use it as your reference example.  You
might become missleaded.  (The existance of this project has leaded to
some confusion in the past, sorry for you beeing trapped as well.)

There are several ways to find out the location of the repository of
some package in question.  For the BioJava example you could do the
following:

  1. BioJava is for *developing* biological applications.  Thus it
     can be found in the according task bio-dev of the Debian Med
     project and is listed on the tasks page:
      http://debian-med.alioth.debian.org/tasks/bio-dev
     You can seek there for the string biojava or you learned via
      $ apt-cache search biojava
     that the name of the package is actually libbiojava-java and
     go staight to
      http://debian-med.alioth.debian.org/tasks/bio-dev#libbiojava-java
     In the right column of the metainformation you will find the
     Link to the repositiory (SVN).

  2. A more generic way (which works for all packages not only
     Debian Med stuff is

      debcheckout libbiojava-java

  3. Also very generic:

      http://packages.debian.org/biojava

     (even if you did not found out the name via apt-cache before)
     Following one link to a certain release will bring you to a
     page which has in the right column links to *.dsc.  This file
     contains information about the repository in the Vcs-fields.

  4. Because I suggested to download the full Debian Med repository
     you can also do

      find trunk -name "*biojava*"

     However, this only works for packages in our SVN (some are
     maintained in Git).

These are just four examples how to find out a repository where a
package is maintained - there are definitely several more.

> find  /srv/home/groups/pkg-escience/htdocs | fgrep biojava

Easy: Because it is NOT there.  Where did you git the impression from
that pkg-escience is connected with biojava?  We should fix this source
of information.
 
> Where do I find the dot deb file for tm-align?

Well, I do not know what you mean by "dot deb" file, but if you are
seeking the repository where tm-align is maintained I'll leave this for
you as exercise now (while I'm going on updating tm-align to latest
version ...)

> The packages I am working on are stored in
> http://www.bioinformatics.org/strap/debian/ They are already
> working and above URL can be added to /etc/apt/sources.list for testing

While this is definitely interesting you must know that everybody of us
has some certain job to do.  Chances that somebody is waiting for
anybody to recommend some repository to browse are quite low.  It works
much better if you say:  My next target is program X and I have the
following question.  I'm pretty sure that you will get a helpful answer
in the next 24 hours (at least).

Kind regards and I really hope that I did not pushed to many information
in one rush onto you

      Andreas.
 

[1] http://www.debian.org/doc/manuals/maint-guide/ 

-- 
http://fam-tille.de
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