Biodoop-BLAST

Biodoop-BLAST is a wrapper-based MapReduce implementation of BLAST for Hadoop. It is based on Biodoop’s core component, in turn based on the Pydoop API for Hadoop.

Installation:

1. install Biodoop core

2. get biodoop-blast from the download page

3. unpack the biodoop-blast tarball, move to the distribution directory and run:

   python setup.py install

   for a system-wide installation, or:

   python setup.py install --user

   for a local installation

Usage

Here is a quick usage example that can be run on a laptop:

$ start-all.sh
$ hadoop dfsadmin -safemode wait
$ wget ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/chromosomes/*random*
$ zcat chr*.gz >genome
$ formatdb -p F -o T -i genome
$ tar cf genome.tar genome.*
$ cat >query.fa
>q1
ATCGCCTCTCCCGACCGAGCCTTCATGGGAGTCCCGCGGGAGCTGCTCCC
>q2
TAGAAACTTGCTATTTCAAGTATTGTCATCACCTGGGATCTTGCTCGAAT
$ biodoop_blast -o output.csv -p blastn -d genome query.fa genome.tar