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Re: Staden on Ubuntu

On Tue, 4 Nov 2008, Lelanthran Manickum wrote:

This is my first posting to this list, so please forgive any breach of etiquette I may

There is no need to apologize for people who have done some work and are
seeling for elp or advise.  Thanks for informing our list about your work.

I've debianised staden 1.7.0 and placed it here.

Great - but you seem to have forgot to insert a link.

Unfortunately, I'm still working on a
few things:
1. Generating the correct diff from the upstream package.

What exactly do you mean by "generating the correct diff".  If you are
using dpkg-buildpackage, debuild or something like this the diff.gz and
the *.dsc file which belong to the orig.tar.gz source will be generated

Or are you rather refering to the diffs you are creating in the debian/
packaging directory by using tools like dpatch or quilt.  In the Debian
Med team we have a slight preference of quilt.

Please be a little bit more verbose to enable us to help you effectively
(and do not hestitate to ask if in case you do not understand what I wrote

Perhaps for a first shot reading


might be helpful.

2. Fixing AMD64 breakages.

I'd suggest reporting these problems upstream.  I have learned that
upstream is quite responsive and is definitely interested in problems
concerning AMD64.

3. Generating a seperate staden-doc package.

This would be easy once you provide the URL to your work.  We have
a lot of examples you can follow.  You might also consider using our
common packaging SVN.  If you check in your work we could easily add
things you feel not able to do yourself.  This has turned out quite
effective in the past.

4. Generating a .profile just for ubuntu so that the default .profile
    is not needed.

This seems to be a Staden specific .profile, right?  I have to admit
that I did not yet dived into Staden deeply enough to comment on this.
If it is something about configuration it should be moved to
/etc/staden/profile - but this is just a wild guess for the moment.

It is, I hope, usable but I'm not a molecular biologist so I'm not even sure that it
works correctly just yet.

Same for me.  I'm a physicist and have to rely on tests of the users
of the packages.

I've used only those packages it came with because I was not
certain that it would work with the system-installed packages. I hope, after it is
verified that the staden on launchpad ppa works, that I can do away with the building
of io-lib and instead use the provisional io-lib from debian-med.

If I remember right Staden needs io-lib and thus we tried to start with
io-lib first.  We tried to separate this lib (well a lib means it is useful
for more than one application (not only Staden) and if I'm not missleaded
there are other applications just do so) to enable more flexibility and
avoid confusion between different versions of one lib in different applications.
Moreover io-lib is a very bad name (I think upstream agreed to this).  So
we added at least 'staden-' as prefix and tried to add a patch which


Once this is done we wanted to proceed with Staden.  So far for a short
explanation of our strategy.  If you think you see a better way to
get Staden packaged this is fine as well.

Lastly, is there a test suite I can run against staden so that automated testing can
take place? It would be great if I could simply rebuild, run the tests and diff the
output of the tests with the previous build.

I do not know such a testsuite - this question might most probably
be answered by upstream staden developers.

Kind regards and thanks for your interest in Debian Med



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