h_blast¶

Hadoop Blast

Runs BLAST on a hadoop cluster

Commands¶

clean: Remove all job data, not the Moa job itself, note that this must be implemented by the template.
run: Similar to a normal blast, but now running on an hadoop cluster

db: Location of the blast database

type: file

default: ``

optional: False
eval: e value cutoff

type: float

default: 1e-10

optional: True
hadoop_base: location of the hadoop installation

type: directory

default: ``

optional: False
hdfs_base: htfs://SERVER:PORT for the hdfs filesystem, defaults to “hdfs://localhost:9000”

type: string

default: hdfs://localhost:9000

optional: True
input_dir: location of the hadoop installation

type: directory

default: ``

optional: False
input_extension: input file extension

type: string

default: fasta

optional: True
nohits: number of hits to report

type: integer

default: 50

optional: True
nothreads: threads to run blast with (note the overlap with the Make -j parameter)

type: integer

default: 1

optional: True
program: blast program to use (default: blastn)

type: set

default: blastn

optional: True