Re: [Cdk-devel] Re: Bringing Bioclipse to Debian

[Egon W. <e.w...@sc...>]

On Wednesday 07 December 2005 16:49, Daniel Leidert wrote:
> X-post to bioclipse, jmol-, cdk-devel list
> BCC to Egon and Stephan
> please answer to the list(s), fitting your answer (I don't need a CC)
>
> First, sorry for the late answer Egon.

No worries.

> Am Dienstag, den 22.11.2005, 14:41 +0100 schrieb Egon Willighagen:
> > as you might know, Eclipse runs with free VMs in Debian GNU/Linux, and
> > Bioclipse runs quite well too, except for the plugins that embed AWT
> > stuff (see other email).
> >
> > I've just been talking to Stephan Michels, who actually contributed to
> > the CDK in the past, and now happens to one of the Debian Java
> > Maintainers doing Debian's Eclipse packages...
> >
> > OK, since Bioclipse almost runs with with free java tools, it can become
> > part of Debian itself (main),
>
> It must completely depend on packages in main to be allowed to go into
> main.

With 'almost' I meant: Bioclipse itself requires only free java tools. Some 
plugins may require non-free stuff (bc_jmol and bc_jcp) and this needs to be 
explored. Those would need to go into contrib.

But to make it clear, bioclipse and bc_cdk:
- can be build with free tools from main (as the build process matches that of
  eclipse)
- can run with free tools from main (I have run it with jamvm and classpath)

> > and making it straightforward for me to add it to
> > the live chemblaics CD I want to release early next year for demoing our
> > favorite software on our friends laptop.
> >
> > Now, Stephan is interested in making debs. Daniel, I was hoping you could
> > help out here too, because the Jmol/JCP plugin debs will depend on debs
> > for Jmol, CDK and JChemPaint... I've done deb packaging in the past too,
> > so can offer testing etc here too...
>
> No problem with that. The whole work is available to the public (ok,
> last solutions are still on my local systems, but if interested I can
> put them online). It would like to see it in Debian. Today I again got
> post asking, why several packages are not part of it :)

Please do put them online, possibly with a brief explanation on how people can 
build the packages from the deb-src sources. I really interested in getting
things ready for debian, (k)ubuntu and the knoppix-based chemoinformatics live 
CD I want to have ready in May 2006.

> > Some questions I currently have (Stephan, Daniel, others, please add
> > yours): - how can be build the things from the command line?
>
> Sorry, I don't understand. What do you mean with "build the things from
> the command line"?

We need a build process for bioclipse framework and the bioclipse plugins.
This will require to build them from the command line, i.e. using the default
Debian build process/daemons.

> > - can we do without the SWT/AWT bridge, which is not available from free
> > tools yet? (see other email)

The SWT_AWT bridge uses com.sun classes. A bug has been filed against Eclipse 
for this. Not sure of the current status of this bug. See [1].

> > - can we resolve the circular dependencies between the current Jmol/CDK
> > debs?
>
> That's a question for upstream. 

Upstream: that's me right?

> The current solution is, that there is a 
> target in Jmol's build.xml to make a package for the jmolApis.jar and
> jmolIO.jar (IIRC you wrote that). But it still requires heavy patching.

Can you point out to me what patching you need to do, then I can fix things 
upstream.

> It would be better to find a clear solution, which can be implemented in
> upstream, e.g. moving the cyclic stuff to the cdk sourcs and build
> cdk-jmol.jar. And BTW: There is another cyclic dependency between JoeLIB
> and cdk (cdk-libio.jar).

OK, lets disregard JOELib for now, as the future of that project is 
(unfortunately) uncertain at this moment...

E.

1.http://developer.classpath.org/mediation/FreeSWTTestApps

-- 
Egon Willighagen
http://chem-bla-ics.blogspot.com/