[BioRuby] GSoC week 2 status report

[John Woods]

If I can just suggest, there's a startup pitch out there which was formerly
known as Happy Science Coding, now Appsoma, which lets you run Ruby code on
Rackspace instances.

It may or may not be appropriate for what you want to do. It's not EC2, but
it is a VM (right?).

http://appsoma.com/

It's still a bit buggy with Ruby. If you have trouble, email Zack (see the
"About us" page). He's fairly responsive.

John
SciRuby

On Tue, May 22, 2012 at 4:21 AM, Raoul Bonnal <bonnal at ingm.org> wrote:

> Hi Clayton,
> Well done and thanks for your contributes to bioruby and jruby community.
>
> For you computing issue I have two solutions:
> 1) I can create a VM and give you the access, I need to contact my IT dep.
> 2) Could Amazon provide some VM for our students?
>
>
>
> On 21/05/12 17.50, "Clayton Wheeler" <cswh at umich.edu> wrote:
>
> > Hi all,
> >
> > Here's my report on last week's work:
> >
> > http://csw.github.com/bioruby-maf/blog/2012/05/21/week_2_progress/
> >
> > This was my second week of work on my GSoC project, and the last week of
> the
> > Œcommunity bonding¹ period before the official start of coding. A major
> focus
> > of mine was BioRuby¹s phyloXML support; it uses libxml, which has been
> causing
> > unit test failures under JRuby. In the end, the best course of action
> seemed
> > to separate the phyloXML support as a separate plugin, which I have done
> as
> > the bio-phyloxml gem. This will remove BioRuby¹s dependency on XML
> libraries
> > entirely and that JRuby issue along with it. At the same time, users of
> the
> > phyloXML code should be able to continue using it with no substantive
> changes.
> >
> > Separately, I began porting this phyloXML code to use Nokogiri instead of
> > libxml-ruby, but ran into difficulties with this effort. While it is
> possible,
> > and the library APIs are very similar, the code uses relatively
> low-level XML
> > processing APIs in ways that seem to be sensitive to subtle differences
> in
> > text node and namespace semantics between the two libraries. Substantial
> > restructuring of the code and the addition of quite a few unit tests
> might be
> > necessary to carry out such a port with confidence that the resulting
> code
> > would work well.
> >
> > Also, someone else submitted a JRuby patch for JRUBY-6658, one of the
> major
> > causes of BioRuby¹s unit test failures with JRuby; once a fix is
> integrated,
> > we¹ll be close to having all the tests passing under JRuby.
> >
> > I identified another JRuby bug, JRUBY-6666, causing several unit test
> > failures. This one affects BioRuby¹s code for running external commands,
> so it
> > would be likely to be encountered in production use. For this one, I also
> > worked up a patch.
> >
> > I also spent some time preparing a performance testing environment, for
> > evaluating existing MAF implementations as well as my own. This will be
> > important, since I will be considering the use of an existing C parser.
> I will
> > also want to ensure that the performance of my code is competitive with
> the
> > alternatives. Lacking any hardware more powerful than a MacBook Air, I am
> > setting this up with Amazon EC2. To simplify environment setup, I¹ll be
> using
> > Chef. I¹ve already set up a Chef repository with configuration logic,
> and some
> > rudimentary code to streamline launching Ubuntu machines on EC2 and
> > bootstrapping a Chef environment. To save money, I plan to make use of
> EC2
> > Spot Instances, which are perfect for instances that only need to run
> for a
> > few hours for batch tasks.
> >
> > Clayton Wheeler
> > cswh at umich.edu
> >
> >
> >
> >
> > _______________________________________________
> > BioRuby Project - http://www.bioruby.org/
> > BioRuby mailing list
> > BioRuby at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioruby
>
>
>
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