[Debian-med-packaging] Help needed for gatk

[Andreas Tille]

Hi Andrew,

On Wed, Jan 27, 2016 at 02:52:55PM -0800, Andrew Schurman wrote:
> On Wed, 2016-01-27 at 15:08 +0100, Andreas Tille wrote:
> > Reading "<goal>compile</goal>" and "<goal>link</goal>" would tell me
> > that these are not needed only for testing, right?
> 
> Don't confused <goal/> with <phase/>. Goals are named subroutines from
> the plugin. Phases are standard Maven names. If you prefer, goals tell
> Maven what to use and phases tells it when to build. Check out the
> build lifecycle [1] for more info. All of the test-y phases have `test`
> in their name.
> 
> Goals can also automatically bind to phases if <phase/> is omitted, in
> which case you'd have to check the plugin documentation to see exactly
> which phase its bound to.
> 
> It pretty safe to say the `compile` goal of the maven-scala-plugin
> binds to the compile phase, so this plugin is needed (it's just
> coincidence they are named the same). As for the maven-junction-plugin, 
> it's phase is set to none. So the plugin won't be used regardless of it
> listing the `link` goal. You just have to be careful that profile
> activations or other configuration don't change that phase on you, then
> it may actually be needed (config is merged).

Thanks for the helpful explanation.
 
> > Just to make sure I'm
> > heading in the right direction:
> > 
> >   scala: https://github.com/davidB/scala-maven-plugin
> >    (this seems to be outdated: http://scala-tools.org/mvnsites/maven-
> > scala-plugin/)
> 
> The one from scala-tools.org may appear to be outdated, but it is the
> plugin that's used. The one from github has a different groupId which
> means it could be a fork, a rewrite or something completely different.

As far as I understand its renamed by the same author.  When I try to
find the source of the old named project at

   http://scala-tools.org/mvnsites/maven-scala-plugin/source-repository.html

it leads to a 404 page at Github.  The author David Bernard has renamed
the project.

> It may be easier to stick with plugin that was actually used otherwise
> you'd have to maintain that change.

I perfectly agree - but I have no idea how to find the according source
code.  I feel a bit unsafe to checkout the new repository and checkout
the last commit with the old name.  Or may be I should write a d/watch
file containing


   https://github.com/davidB/scala-maven-plugin/releases?after=3.1.1 .*/archive/v*(2\.[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)


which is a bit weak but fetches (at least at this point in time) the
latest version of scala-maven-plugin 2.x - which seems to be the old
version you were suggesting to use.

Kind regards

      Andreas.

> [1] https://maven.apache.org/guides/introduction/introduction-to-the-li
> fecycle.html



-- 
http://fam-tille.de