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Re: Bug#507436: ITP: jalview -- multiple alignment editor

On Tue, 13 Jan 2009, Vincent Fourmond wrote:

 About the repository, I think the best is pkg-java, as the skills
required are more on the Java side than on the Biological side - but
please correct me if I'm wrong.

Well, there is no right or wrong - finally we have to store the
packaging stuff in a publicly available repository.  Via Vcs tags
we will find the location and the upcoming 'mr' tool will probably
help fetching stuff from different repositories.  So I would just
*ask* on pkg-java whether they like the idea to maintain the
package there (yes, Java knowledge on Debian Med is not so wide
spread).  If there is no response this is probably not the proper
place.  Perhaps Steffen might like to say something more than
 'why isn't anybody mentioning pkg-escience ?'
My answer to this question is simple: This group is not vocal
enough and how can I assume that there is some Java competence?

The main problem is that it has loads
of dependencies:

12:40 fv@Vncent ~/tmp/jalview find -name '*.jar'

http://www.castor.org/ (not yet packaged) ?


libcommons-logging-java ?


libcommons-discovery-java ?




libgnu-regexp-java | libjrexx-java libjrexx-java | liboro-java | libregexp-java ?


https://saaj.dev.java.net/ (not packaged yet) ?
Seems to have to do something with SOAP, perhaps there are alternative implementations
like the packaged libaxis-java ???


Reading http://de.wikipedia.org/wiki/JAX-RPC the package
might provide what we need.  At least the package contains /usr/share/java/jaxrpc.jar


$ apt-file search '/mail.jar'
jspwiki: /usr/share/jspwiki/WEB-INF/lib/mail.jar  <- probably not
roxen4: /usr/share/roxen4/java/classes/mail.jar

Perhaps this might be a reasonable solution:

libgnumail-java: /usr/share/java/gnumail.jar


libaxis-java: /usr/share/java/axis.jar


http://www.vamsas.ac.uk/ ?
--> If this is a precondition for JalView Debian Med should
    perhaps concentrate on this part.  Unfortunately the web
    page is a little bit sparse about vamsas itself - but
    seems deeply connected with JalView.  I will have a look
    at the other free part Topali (AstexViewer seems to
    be non-free)


We have an inofficial package of an outdated version of jmol:


Daniel, any news from Jmol?


libgnujaf-java: /usr/share/java/activation.jar


javahelp2: /usr/share/java/jhall.jar


libxerces2-java: /usr/share/java/xercesImpl.jar


libxalan2-java: /usr/share/java/xml-apis.jar
maven2: /usr/share/maven2/lib/xml-apis.jar


liblog4j1.2-java  (and others)


No idea - perhaps
ist helpful.  While having no idea what maven2 might be at all I have read
this keyword on the Debian-Java list recently quite frequently.


No idea.


see castor above




proguard: /usr/share/java/proguard.jar


 I'll start to sort it out this week-end. You can join in too,s

Just joined. ;-)

instance, to see which of those are really necessary, file ITP, block
this bug by the ITPs (CCing this bug), and package them (and their
dependencies...). I guess the best would be to use this bug
mailing-list for coordination. I think it is possible we can get rid
of the dependencies from the utils/ directory...

Lets see.  I'm occupied with other tasks for this afternoon, but may
be I might provide some more info later.

Kind regards



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