README
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Blast DB Indexer Mini Pipeline for Galaxy v. 0.1
(c) 2011 Jacob Israel Cervantes Luevano
http://www.langebio.cinvestav.mx
http://www.langebio.cinvestav.mx/bioinformatica/jacob
Langebio Cinvestav, Dept. of Bioinformatics 
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TABLE OF CONTENTS
I.   INTRODUCTION		
II.  DOCUMENTATION
III. CONTACT INFO
IV.  REPORTING BUGS

Project WebSite: http://www.jacob-israel.com.mx/bio/blog

I. INTRODUCTION
script allows to format blast databases, set galaxy reference format and to create galaxy reference megablast loc files

II. DOCUMENTATION
Usage:

$ set_galaxy_blastdb.sh -help
$ set_galaxy_blastdb.sh -fasta filename -p T|F -n blastdb_name -fastadesc ncbi-gk|other

where :

-fasta filename
-p T ; if your database are protein sequences
-p F ; if your database are nucleotide sequences
-n blastdb_name ; set database filename for Galaxy Loc File
-fastadesc ncbi-gk ; option if your fasta ID is like gi|gi-number|gb|accesión|locus
-fastadesc other ; your own sequence IDs

to run :
$ ./set_galaxy_blastdb.sh -fasta /media/xlinux/genomes/galaxy/palomero/megablast/genome.fasta -p F -n my-genomedb-name -fastadesc ncbi-gk

III. CONTACT INFO
Feel free to contact me if you have any comments, suggestions, questions, complaints, whatever.

Jacob Israel Cervantes Luevano
Langebio Cinvestav, Dept. of Bioinformatics
Irapuato, Guanajuato México

Email: [email protected]
Email: [email protected]
WebSite: http://www.jacob-israel.com.mx/bio/blog

IV. REPORTING BUGS
Email me please