[BioRuby] ruby BLAST server (web frontend)

[Anurag Priyam]

> cute work.

Thanks a lot Raoul :).

> Just few suggestions.
> you could build a gem and distribute is then with a single executable script "sequenceserver" you can call all other tasks,
> configuration, database or starting the service like we did with biongs; it's a more consistent approach and the end user has a clear reference to your application.

Agreed. And that is our target for the next release.

> Installing it as gem then you need to build a web environment somewhere else but it is quite simple to create a scaffold directory ready to be used by a web server (where you put your configuration/database ref, public, js, css etc.)
> something like:
>
> sequenceserver database_formatter directory_with_fasta_files
> sequenceserver config production --bin="~/ncbi-blast-2.2.24+/bin/" --database="/Users/me/blast_databases/"
> sequenceserver start

This looks quite good. I will keep this in mind when pushing forward a
gem release.

>> then if your application runs on ruby 1.87, try REE with passenger and nginx, in my opinion is the easiest web server (NGINX) with high level of performances http://www.modrails.com/
>
> if you need help to configure nginx I can give you some hint or example of my config, it works well with rvm as well.

That would be great. We are putting forward a wiki page with
instructions on deploying SequenceServer on Apache, and Nginix. I am
almost done adding instructions for Apache, but I am not sure how to
do it for Nginix.

> could this became a bioruby plugin ?

So, then would it become bio-sequenceserver? IMO, it doesn't logically
fit in as a BioRuby plugin, as in it doesn't depend on BioRuby. And
BioRuby is more like library but SequenceServer is more like an end
product. Not sure though :-|.

-- 
Anurag Priyam
http://about.me/yeban/