[BioRuby] Bioruby PhyloXML update
Diana Jaunzeikare
rozziite at gmail.com
Sun May 31 01:36:52 UTC 2009
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.
>>
>>
>
>
>
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