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Re: questions regarding packaging

On Fri, Nov 18, 2011 at 08:47:31PM +0100, Dr. med. Christoph Gille wrote:
> Thanks so much for your help with neobio. By watching the changes I
> have learned a lot.  I will use neobio as a template for further
> packages.

No problem - this is the approach we are following here in the team:
Educate more people in packaging and thus strengthen our team.

BTW regarding neobio I also forgot the issue I raised in the very
beginning:  YOu are inventing a version number "1" for some unmaintained
(no upload since 2003), pre-alpha software.[1]  That's simply not
correct and I'd strongly suggest to use the date versioning scheme - in
this case this would be neobio-0.0.20030929.

As an additional note I wonder whether it is a really good idea from a
QA point of view to relay your strap software on unmaintained alpha

> I am planning debian packages for the protein workbench strap and an
> advanced text-viewer.  Both are based on the same jar-file.  Therefore I
> consider three packages - is this the right approach?

It might b a reasonable approach (there is usually no strong right
or wrong) but I admit I can not give a final advise here.  It somehow
depends how much workload will be end up in the additional packages.

>  1. "strap-base" providing the jar-file
>  2. "strap" which depends on strap-base, clustalw  and several others
>  3. "strap-text-viewer" which depends on strap-base and doccat.
>     This will be a text viewer mainly for plain text
>     (but also Winword and perhaps odt and docx)
>     Improved search/highlight, Scriptability and
>     text size up to several 100MB.

If the strap and strap-text-viewer package will only contain wrapper
scripts which call a certain class in the jar file of strap-base I'd
rather recommend to move these wraooers inside the single file.  It is
perfectly OK to have more than one executable in one Debian package.
Bu tI might have a look into you packaging soon and will come up with
a more competent answer thought.
> There is already a preliminary version of strap-base in the svn.
> It does already produce a strap-base_1-1_all.deb file (-:
> Some more questions,
> 1. Strap has several icons, without an explicit copyright -
>    e.g. icons from bioinformatics databases.  Should I better delete
>    all those icons to avoid problems?

If it is not possible to get a valid copyright and license of these
icons it is better to go without them or replace them by free pendants.
> 2. Can I define variables within a code block of a Makefile?
>    For example I wanted to put the output of a find-command in a variable
>    to reuse this output in a later line.

Do you mean something like
MYVARIABLE := $(shell find . -name something )
> 3. Supposed I am in the directory of some package like
>    /trunk/packages/cinema/trunk/.  Is there a simple sequence of
>    commands or a single command to perform all steps: (1)Downloading
>    the orig, (2) compiling and (3) make the cinema-*.deb file?

The downloading is a separate step:

    make -f debian/rules get-orig-source

However (2) and (3) are in most cases on step which is triggered for
instance by


We also usually recommend


which does the build process in a clean chroot environment.  This is
explained in Detail in the Debian Med policy[2].
Hope this helps


[1] http://sourceforge.net/projects/neobio/files/neobio/pre-alpha/ 
[2] http://debian-med.alioth.debian.org/docs/policy.html


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