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Old 12-01-2008, 09:34 AM
Vincent Fourmond
 
Default Bug#507436: ITP: jalview -- multiple alignment editor

Package: wnpp
Severity: wishlist
Owner: Vincent Fourmond <fourmond@debian.org>

* Package name : jalview
Version : 2.4
Upstream Author : Andrew Waterhouse; Jim Procter; David Martin; Geoff Barton
* URL : http://www.jalview.org
* License : GPL (v2 or later)
Programming Lang: Java
Description : multiple alignment editor

JalView is a Java alignement editor that can work with sequence
alignement produced by programs implementing alignment algorithms
such as clustalw and kalign.
.
It has lots of features, and can be considered a decent BioEdit replacement
for Debian systems.


This program is in java and therefore comes with the standard bunch of
java-related problems: binary jars in the source and the like. I haven't
checked yet wether all dependencies are truly free of if they are packaged
for Debian.

I intend to place this package under the juridiction of the debian-java
team, but I am aware it could also belong to the Debian Med Team...

Cheers,

Vincent

-- System Information:
Debian Release: lenny/sid
APT prefers unstable
APT policy: (500, 'unstable'), (500, 'testing'), (500, 'stable')
Architecture: amd64 (x86_64)



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Old 01-13-2009, 12:00 PM
Andreas Tille
 
Default 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'
./lib/castor-1.1-cycle-xml.jar


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


./lib/commons-logging.jar


libcommons-logging-java ?


./lib/commons-discovery.jar


libcommons-discovery-java ?


./lib/wsdl4j.jar


libwsdl4j-java


./lib/regex.jar


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


./lib/saaj.jar


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 ???


./lib/jaxrpc.jar


Reading http://de.wikipedia.org/wiki/JAX-RPC the package
libxmlrpc3-common-java
might provide what we need. At least the package contains /usr/share/java/jaxrpc.jar


./lib/mail.jar


Hmm:
$ 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


./lib/axis.jar


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


./lib/vamsas-client.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)


./lib/Jmol-11.0.2.jar


We have an inofficial package of an outdated version of jmol:

http://debian.wgdd.de/temp/jmol/

Daniel, any news from Jmol?


./lib/activation.jar


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


./lib/jhall.jar


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


./lib/xercesImpl.jar


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


./lib/xml-apis.jar


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


./lib/log4j-1.2.8.jar


liblog4j1.2-java (and others)


./utils/castor-1.1-cycle-codegen-anttask.jar


No idea - perhaps
http://castor.codehaus.org/srcgen-maven-plugin.html
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.


./utils/jhindexer.jar


No idea.


./utils/castor-1.1-cycle-codegen.jar


see castor above


./utils/wsdl4j.jar


libwsdl4j-java


./utils/proguard.jar


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


./utils/roxes-ant-tasks-1.2-2004-01-30.jar
./utils/jalopy/lib/oro-2.0.6.jar
./utils/jalopy/lib/sax-2.0.1.jar
./utils/jalopy/lib/jalopy-ant-0.6.2.jar
./utils/jalopy/lib/log4j-1.2.6.jar
./utils/jalopy/lib/jaxp-1.2.jar
./utils/jalopy/lib/aelfred-1.2.jar
./utils/jalopy/lib/jalopy-1.0b11.jar
./utils/jalopy/lib/jdom-1.0b8.jar
./utils/jhall.jar
./utils/axis-ant.jar

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


Just joined. ;-)


for
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

Andreas.

--
http://fam-tille.de


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