[BioRuby] ruby BLAST server (web frontend)

[Yannick Wurm]

Thanks for the suggestions Raoul,
they could substantially streamline setting things up!

cheers
yannick



On 13 Jun 2011, at 14:17, Raoul Bonnal wrote:

> Dear Yannick and other,
> cute work.
> 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.
> 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
> 
> 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.
> 
> could this became a bioruby plugin ?
> 
> 
> 
> 
> 
> On 13/giu/2011, at 07.49, Yannick Wurm wrote:
> 
>> Dear list & CC-ed,
>> 
>> let me quote a discussion from a while back ( http://answerpot.com/showthread.php?1292835-rails+blast+server ):
>> 
>>> I'd like to set up a small server for people to run BLAST against some of my sequences & see the results. 
>>> GMOD obviously comes to mind, but it seems like overkill. 
>>> And perhaps there is an almost automagic way to do this with ruby on rails. Has anyone done this yet?
>> 
>> 
>> There was no good solution at the time. Anurag Priyam & I have since been working on something that fills this need. Ben Woodcroft has recently been contributing as well. Check:
>> https://github.com/yannickwurm/sequenceserver or http://www.sequenceserver.com
>> 
>> Some things remain to be improved. But globally the software works great. Thus we thought to share our progress on the list that initiated it. An excerpt of the README highlights some features:
>> 
>> Ease of use for biologists:
>> * intuitive and helpful web interface: automatic sequence type detection that helps choose appropriate BLAST method and database types
>> * links to easily download sequences of BLAST hits
>> * support for advanced options.
>> 
>> Rapid deployment for bioinformatics administrators:
>> * assisted formatting of BLAST databases (with sequence type detection)
>> * automatic discovery of formatted BLAST databases during startup
>> * uses ruby's internal web server (on any open port) or Apache
>> * add custom hyperlinks from hits (to your genome browser or custom database).
>> 
>> 
>> We have been using this as the web frontend for our ant genome blast at http://www.antgenomes.org since a few months. 
>> 
>> Comments, suggestions... and contributions are most welcome!
>> 
>> Cheers,
>> 
>> Anurag & Ben & Yannick
>> 
>> 
>> 
>> -----------------------------
>>  Ant Genomes & Evolution 
>> http://yannick.poulet.org
>>    skype://yannickwurm
>> -----------------------------
>> 
>> _______________________________________________
>> BioRuby Project - http://www.bioruby.org/
>> BioRuby mailing list
>> BioRuby at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioruby
> 



-----------------------------
   Ant Genomes & Evolution 
  http://yannick.poulet.org
     skype://yannickwurm
-----------------------------
BLAST @ http://antgenomes.org