[BioRuby] gsoc suggestion: microframework for simple scientific web wrappers

Fri Feb 7 02:28:59 UTC 2014

Sounds cool yannick. Some thoughts:

* the ptools rubygem has a 'which' method, which might be of use.
* the version tool would in itself be useful. Including it in a script to
add a --version flag, automatically working out the version from
rubygems/git commit/whether the repo is dirty/etc. would be pretty cool, as
it would ease documenting versions used.
* bio-commandeer seems of obvious use..

Is there any good markup language for describing program inputs and
outputs? Anything that could be stolen from galaxy?

ben

On 7 February 2014 04:47, Fields, Christopher J <cjfields at illinois.edu>wrote:

> You can always mentor and discuss implementations on this list to get
> others thoughts.  That's the fun of it, both for the student and the
> community.
>
> chris
>
> On Feb 6, 2014, at 6:24 AM, Yannick Wurm <y.wurm at qmul.ac.uk> wrote:
>
> > Thanks, glad you like the idea.
> >
> > The thing is I'm not technical enough to supervise the implementation...
> so I could only co-supervise with the help of a strong technical thinker.
> >
> > This could fit under sci-ruby's remit as well.
> >
> > Cheers,
> > Yannick
> >
> >
> >
> > On 6 Feb 2014, at 06:34, Pjotr Prins <pjotr.public14 at thebird.nl> wrote:
> >
> >> This is a very good idea, and ties in with earlier bio-ngs work and
> >> our future plans in pipeline software management.
> >>
> >> GSoC also likes 'infrastructure' type projects - it was found out the
> >> last summit.
> >>
> >> Do add it to the OBF project proposal list. Also mention bio-ngs and
> >> your project.
> >>
> >> Pj.
> >>
> >> On Thu, Feb 06, 2014 at 12:09:58AM +0000, Yannick Wurm wrote:
> >>> Dear all,
> >>>
> >>> a small thought about a potential GSoC project.
> >>>
> >>> Many bioinformatics software consist in a binary that you run on the
> command line with one or few input files, some parameters and generates
> some output files. Let's consider only software that generates potentially
> human-readable output.
> >>>
> >>> Most of us on this mailing list have no problem running that kind of
> software on the command-line. But for the majority of biologists that's
> still impossible: they need a point and click interface instead.
> >>>
> >>> So if you're the person who needs to implement that point and click
> interface, how do you do it?
> >>> 1. create a wrapper for galaxy [1]. This has become easy.. but puts
> the burden on your enduser to have or set up a galaxy installation (not
> trivial), and the galaxy user experience is debatable.
> >>> 2. use sinatra.rb (we did this for our sequenceserver wrapper for
> blast) - it worked but involved way too much manual labor.
> >>> 3. be old-skool (build your own from php/etc).
> >>>
> >>>
> >>> Clearly 1 isn't always appropriate & locks you into a weird framework,
> and 2. is still to much work. Padrino & rails are overkill for the simplest
> apps. With Ruby providing such great web development frameworks, why isn't
> there an easier/faster way to generate a web wrapper around a piece of
> scientific software?
> >>>
> >>> Perhaps I'm missing something.
> >>>
> >>> Alternatively, creating a "wrapping scientific software" framework
> could be a viable GSoC project.
> >>>
> >>> Build it upon Sinatra, create a rigid framework where the basic
> locations of files that the developer needs to edit are predetermined
> (similarly to rails). Single page/webform for the user to enter data;
> single output/download page after the run was successful. No need to store
> any user-data on the server. The framework should include the following
> features:
> >>> * easy way to verify presence, executability and version of binary (or
> script) that is being wrapped
> >>> * easy way to specify number of input files, and potential constraints
> on them  [this stuff should be specified once; appropriate HTML should be
> auto-generated (bootstrap)].
> >>>   * most basic constraints: size and/or extension
> >>>   * more advanced constraints: user-extensible function that verifies
> the format
> >>> * easy way to specify possible parameters and constraints on their
> types
> >>> * easy way to show/include local data (HMM models, sequence databases
> etc...)
> >>> * easy way to make text-output look good
> >>>   * eg. inserting specific headers or indexing at specific regexps
> (for table of contents)
> >>>   * eg. csv output should be shown as a table
> >>>
> >>> I'm not the best qualified person to consider exact implementation
> details, but if someone wants to go ahead with it I'm happy to provide more
> general thoughts.
> >>>
> >>> Cheers,
> >>>
> >>> Yannick
> >>>
> >>> [1]: http://galaxyproject.org
> >>>
> >>>
> >>> -------------------------------------------------------
> >>> Yannick Wurm - http://yannick.poulet.org
> >>> Ants, Genomes & Evolution ??? y.wurm at qmul.ac.uk ??? skype:yannickwurm
> ??? +44 207 882 3049
> >>> 5.03A Fogg ??? School of Biological & Chemical Sciences ??? Queen
> Mary, University of London ??? Mile End Road ??? E1 4NS London ??? UK
> >>>
> >>>
> >>> _______________________________________________
> >>> BioRuby Project - http://www.bioruby.org/
> >>> BioRuby mailing list
> >>> BioRuby at lists.open-bio.org
> >>> http://lists.open-bio.org/mailman/listinfo/bioruby
> >
> >
> > _______________________________________________
> > BioRuby Project - http://www.bioruby.org/
> > BioRuby mailing list
> > BioRuby at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioruby
>
>
> _______________________________________________
> BioRuby Project - http://www.bioruby.org/
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby
>

-- 
--
Ben Woodcroft
http://ecogenomic.org/users/ben-woodcroft <http://www.ecogenomic.org/>