Removed plain uncompiled c++ code from ensembl binary (Was: new member introduction)

[Andreas Tille <andreas@an3as.eu>]

On Fri, Dec 09, 2011 at 01:00:48PM +0000, Nick James wrote:
> >I'm tempted to kick all files matching "*.h" and "*.cpp" from the binary
> >package where these are pretty useless.  This would solve the lintian
> >warnings
> >
> >W: libensembl-core-perl: executable-not-elf-or-script usr/share/ensembl/ensembl/misc-scripts/alternative_splicing/AltSplicingToolkit/src/util/StringUtil.h
> >W: libensembl-core-perl: executable-not-elf-or-script usr/share/ensembl/ensembl/misc-scripts/alternative_splicing/AltSplicingToolkit/src/util/StringUtil.cpp
> >
> >What do you think?
> This is used for loading data into ensembl again, and is not needed
> for the functioning website ( as with run_me in the previous post).
> However, this would be a useful resource for anyone wanting to load
> variation data into their own copy of Ensembl, so I think it should
> be kept in some form. I think you mean just keep the binaries and
> not the source, right?

I investigated things a bit and realised that the binary in this
subdirectory is actually not builded at all in our current packaging.
So either this was intended and thus correct we do not need the sources
in some hidden place in the binary or we just need to find a way how
to properly build the resulting binary.  I just implemented the first
variant (because it's more simple) in

http://anonscm.debian.org/viewvc/debian-med/trunk/packages/ensembl/ensembl/trunk/debian/rules?r1=8979&r2=8980&;

What do you think?

BTW, a very valuable thing to do would be to write a man page for

  ensembl-bin: binary-without-manpage usr/bin/calc_genotypes

If you have no idea how to do this just say so - there are some hints
how to do this for a start.  YOu will also find a lot of examples in
Debian Med SVN via

  find trunk/packages -name "*.[1-9]"

We might make upstream happy (and thus they might be more easier willing
to accept other patches) if we provide them this piece of documentation.

Kind regards

       Andreas.

-- 
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