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>
debuild
> 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
Andreas.
--
http://fam-tille.de
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