[BioRuby] Bioruby PhyloXML update

[Diana Jaunzeikare]

I looked at libxml-jruby and tried to install it, but i get "no such file to
load -- java" on the line "require 'java'". I have both jruby and java
installed. I also have .../jruby/bin directory in my $PATH.

Any suggestions?

Diana

On Wed, May 27, 2009 at 3:30 AM, Raoul JP Bonnal <bonnalraoul at ingm.it>wrote:

> Hi Diana,
> a portability issue.
> Have you guys verified if LibXML::XML is it running on JRuby ? I don't
> think so because it's implemented in C. A solution could be
> this http://github.com/mguterl/libxml-jruby/tree/master but today I can't
> access to it, probably due to my network problems.
>
> Some test, 1 year ago - last post -:
>
> http://www.nabble.com/comparing-xml-parsing-in-JRuby-and-MRI-td16268560.html#a16268560
>
> this is the test code - good portability example too - :
>
> https://svn.concord.org/svn/projects/trunk/common/ruby/xml_benchmarks/xml_benchmarks.rb
>
> Cheers.
>
> Diana Jaunzeikare ha scritto:
>
>> Hi all!
>>
>> Here is what was done during community bonding period:
>>
>>   - subscribed to mailing lists
>>   - created a blog <http://latvianlinuxgirl.blogspot.com/>
>>   - got familiar with Git (this was particularly useful:
>>   http://www.gitcasts.com/posts/railsconf-git-talk )
>>   - created GitHub account and forked bioruby project.
>>   - made first commit by adding sample phyloxml data files from
>>   www.phyloxml.org
>>   - reviewed BioPerl phyloXML implementation (also
>>   http://www.bioperl.org/wiki/HOWTO:Trees )
>>   - got familiar with libxml-ruby. Wrote simple program using both
>>   LibXML::XML::Reader and LibXML::XML::SAXParser to parse a simple xml
>> file.
>>   - reviewed Ruby classes - Bio:Tree, Bio::Pathways
>>   - After discussions in mailing lists it has been agreed to use
>>   LibXML-ruby library, the LibXML::XML::Reader class
>>
>>
>> This weeks plan:
>>
>>   - Start writing parser using LibXML::XML::Reader. It should return a
>>   Bio::Tree object.
>>   - Implement function next_tree to parse and return the next phylogeny.
>>   - Design Tree::Node object for containing phyloxml elements.
>>   - Start mapping phyloxml elements to Bio::Tree::Node, start with
>>   taxonomy, branch_length, scientific_name
>>   - Write simple unit tests.
>>
>>
>
>
>