[Debian-med-packaging] Help needed for gatk

[Andrew Schurman]

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).

> 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    (this seems to be outdated: http://scala-tools.org/mvnsites/maven-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The one from scala-tools.org may appear to be outdated, but it is the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.
It may be easier to stick with plugin that was actually used otherwise
you'd have to maintain that change.


Andrew

[1] https://maven.apache.org/guides/introduction/introduction-to-the-li
fecycle.html
-------------- next part --------------
A non-text attachment was scrubbed...
Name: signature.asc
Type: application/pgp-signature
Size: 819 bytes
Desc: This is a digitally signed message part
URL: <http://lists.alioth.debian.org/pipermail/debian-med-packaging/attachments/20160127/536b0762/attachment.sig>