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Re: questions regarding packaging

On Sun, Nov 20, 2011 at 08:07:42PM +0100, Dr. med. Christoph Gille wrote:
> Neobio is used in Strap to make alignments of two sequences.  Since it
> is a java library, it avoids the overhead of starting a huge program
> like clustalw.  I would not mind using any other library, but I have
> not spotted an appropriate library for aligning sequences which is (1)
> in java (2) runs fast and (3) is already packaged in debian. If
> someone knows an existing debian package, I could use it in Strap.
Hope somebody is able to comment on this. 
> >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 instance by
> >    debuild
> I tested these two commands on some packages like bowtie but it did
> not work:

Well, it is rather like:

   apt-get source bowtie
   cd bowtie-<version>

> c@n:~/testSvn2/trunk/packages/bowtie/trunk$ debuild
>    This package has a Debian revision number but there does not seem to be
>    an appropriate original tar file or .orig directory in the parent directory;
>    (expected one of bowtie_0.12.7.orig.tar.gz, ...

I'm afraid I'm not sure if I understand what you really did.
Just make sure that the original tarball is located as if
you would have used "apt-get source <package_name>" and you
are calling (p)debuild from inside the unpackaged directory.
> I copy the file from tarballs and try again
> c@n:~/testSvn2/trunk/packages/bowtie/trunk$ ln
> ../tarballs/bowtie_0.12.7.orig.tar.gz ..
> c@n:~/testSvn2/trunk/packages/bowtie/trunk$ debuild

I can confirm that bowtie builds fine for me - so something seems to be
wrong at your side.
> For neobio, the following sequence works however:
> being in trunk/packages/neobio/
> c@n:~/testSvn2/trunk/packages/bowtie$ tar xzf
> tarballs/neobio_0.0.20030929.orig.tar.gz
>   cd neobio-0.0.20030929.orig/
>   ln -s ../trunk/debian/ .
>   fakeroot ./debian/rules
>   fakeroot ./debian/rules binary

Hmmm, in principle debuild does something like this and I guess you need
to understand how it fails on your side.
> ------------------------------------------------
> >Do you mean something like
> >MYVARIABLE := $(shell find . -name something )
> Yes, but unfortunately it seems to work only in the preample of the rules file
> but not after a target.
> For example the following in rules produces an error:
> override_dh_auto_build:
> 	echo override_dh_auto_build
> 	MYVARIABLE := $(shell find . -name something )

I have seen your rules file and I can confirm that this variable setting
is exactly intended for the preamble settings - because I assumed thyt
you were asking me exactly about this.  However, what you actually want
to approach is shell scripting and this works like

   MYVARIABLE=`find . -name something` ; echo $$MYVARIABLE

(please mind the double $$ to tell make variables and shell variables
appart) or more straigthforeward

   echo `find . -name something`

There is no reason to use some variable.
> This yields the output
>    ./debian/rules:16: *** commands commence before first target.  Stop.

Yes, that's usual make behaviour.

Kind regards



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