Re: Source code of phyutility
On Mon, Jan 30, 2012 at 12:31:04PM -0500, Stephen Smith wrote:
> There is now a basic ant build file included and I released a new version.
Thanks a lot, that's very helpful.
> One question is that typically, so that it can be run like a normal
> program without the java -jar phyutlity.jar, I encourage using a
> shell script that just has
> java -Xmx2g -jar LOCATION/phyutility.jar $*
>
> The memory option is something that needs to be available to be
> changed if need be as well. Anyway, not sure if that is easy to have
> in the ant build or not, but I am not familiar with a good way. If
> you know of a good standard way to do that (generate that script and
> put it somewhere in the PATH), I am happy to include that as part of
> the build, otherwise, you can do it in the package installation.
I do not know whether there is a way to use ant for the script
generation and I have to admit that I'm most probably not the correct
person to ask such things. I have close to no Java experience and just
dived a bit into it because we have a lot pf phylogeny software around
which is just written in Java and we simply need it in Debian. So
anybody needs to tackle this and it turned out that this anybody is just
me. For tricky Java questions I'm consulting the Debian Java team and
I observed that they provide such simple scripts just in their package
installations which is simple enough.
> Let me know what else you need.
The real problem with phyutility is derby.jar. Debian requires the code
for all binary code inside the distribution. So we usually need to do
package those JARs from scratch as extra packages and the use the Debian
packaged version. While there were some intends to package Derby in the
past but with no visible outcome so far. That's a bit unfortunate
because I as a beginner do not want to dive into this one.
> I am an Arch and Ubuntu user so good to see packages being built
So it might happen it ends up in Debian non-free section because of the
Derby issue - I personally have no idea how this propagates to Ubuntu
but using it from the Debian mirror in non-free should be no issue under
recent Ubuntu versions.
Thanks for your support
Andreas.
--
http://fam-tille.de
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