scbi_distributed_blast

DESCRIPTION:

scbi_distributed_blast is a simple distribution mechanism for blast+ made on top of scbi_mapreduce. With scbi_distributed_blast you can perform distributed blasts using a cluster, a set of machines of your network or your own multi-core personal computer. It uses the same blast+ that you have already installed.

FEATURES:

  • Automatically distribute blast+ jobs against multiple computers.

  • Sequences are sent in chunks.

  • scbi_distributed_blast uses scbi_mapreduce and thus is able to exploit all the benefits of a cluster environment. It also works in multi-core machines and big shared-memory servers.

SYNOPSIS:

Once installed, scbi_distributed_blast is very easy to use. To launch it locally in your own personal computer using 8 cores, you can do:

$> scbi_distributed_blast -w 8 'full_blast_cmd'

Where full_blast_cmd is the blast+ cmd that you would write to execute your desired blast search. Eg.:

$> scbi_distributed_blast -w 8  'blastn -task blastn-short -db my_db.fasta -query ~/seqs/sample.fasta -outfmt 6 -out output_file'

Sequences are sent in chunks of 100, but you can change this value by using the -g parameter:

$> scbi_distributed_blast -w 8 -g 200 'blastn -task blastn-short -db my_db.fasta -query ~/seqs/sample.fasta -outfmt 6 -out output_file'

To get additional help:

$> scbi_distributed_blast -h

CLUSTERED EXECUTION:

To take full advantage of a clustered installation, you can launch scbi_distributed_blast in distributed mode. You only need to provide it a list of machine names (or IPs) where workers will be launched (be sure you followed the clustered installation instructions).

Setup a workers file like this:

machine1
machine1
machine2
machine2
machine2

And launch scbi_distributed_blast this way:

$> scbi_distributed_blast -w workers_file -s 10.0.0 'blastn -task blast-short'

This will launch 2 workers on machine1 and 3 workers on machine2 using the network whose ip starts with 10.0.0 to communicate.

REQUIREMENTS:

  • Ruby: 1.9.2 recommended.

  • Blast plus 2.24 or greater (prior versions have bugs that produces bad results)

REQUIREMENTS INSTALL:

You can skip this section if you have ruby and blast+ already installed.

Installing Blast

*Download the latest version of Blast+ from ftp.ncbi.nlm.nih.gov/blast/executables/release/LATEST/ *You can also use a precompiled version if you like *To install from source, decompress the downloaded file, cd to the decompressed folder, and issue the following commands:

./configure
make
sudo make install

Installing Ruby 1.9

*You can use RVM to install ruby:

Download latest certificates (maybe you don’t need them):

$ curl -O http://curl.haxx.se/ca/cacert.pem 
$ export CURL_CA_BUNDLE=`pwd`/cacert.pem # add this to your .bashrc or

equivalent

Install RVM:

$ bash < <(curl -k https://rvm.beginrescueend.com/install/rvm)

Setup environment:

$ echo '[[ -s "$HOME/.rvm/scripts/rvm" ]] && . "$HOME/.rvm/scripts/rvm" # Load RVM function' >> ~/.bash_profile

Install ruby 1.9.2 (this can take a while):

$ rvm install 1.9.2

Set it as the default:

$ rvm use 1.9.2 --default

INSTALL:

Install scbi_distributed_blast

scbi_distributed_blast is very easy to install. It is distributed as a ruby gem:

gem install scbi_distributed_blast

This will install scbi_distributed_blast and all the required gems.

CLUSTERED INSTALLATION

To install scbi_distributed_blast into a cluster, you need to have the software available on all machines. By installing it on a shared location, or installing it on each cluster node. Once installed, you need to create a init_file where your environment is correctly setup (paths, BLASTDB, etc). E.g.:

export PATH=/apps/blast+/bin
export BLASTDB=/var/DB/formatted
export SCBI_DISTRIBUTED_BLAST_INIT=path_to_init_file

And initialize the SCBI_DISTRIBUTED_BLAST_INIT environment variable on your main node (from where SCBI_DISTRIBUTED_BLAST_INIT will be initially launched):

source path_to_init_file

If you use any queue system like PBS Pro or Moab/Slurm, be sure to initialize the variables inside each submission script.

NOTE: all nodes on the cluster should use ssh keys to allow scbi_mapreduce to launch workers without asking for a password.

SAMPLE INIT FILES FOR CLUSTERED INSTALLATION:

Init file

$> cat ~/scbi_distributed_blast_init_env 

export BLASTDB=/BLAST_DATABASES/
export SCBI_DISTRIBUTED_BLAST_INIT=~/scbi_distributed_blast_init_env

PBS Submission script

$> cat sample_work.sh 

# 40 distributed workers and 1 GB memory per worker:
#PBS -l select=40:ncpus=1:mpiprocs=1:mem=1gb
# request 10 hours of walltime:
#PBS -l walltime=10:00:00
# cd to working directory (from where job was submitted)
cd $PBS_O_WORKDIR

# create workers file with assigned node names

cat ${PBS_NODEFILE} > workers

# init scbi_distributed_blast
source path_to_init_file

time scbi_distributed_blast -s 10.0.0 -w workers  'blastn -task blastn-short -db my_db.fasta -query ~/seqs/sample.fasta -outfmt 6 -out output_file'

Once this submission script is created, you only need to launch it with:

qsub sample_work.sh

MOAB/SLURM submission script

$> cat sample_work_moab.sh

#!/bin/bash 
# @ job_name = STN
# @ initialdir = .
# @ output = STN_%j.out
# @ error = STN_%j.err
# @ total_tasks = 40
# @ wall_clock_limit = 10:00:00

# guardar lista de workers
sl_get_machine_list > workers

# init scbi_distributed_blast
source path_to_init_file

time scbi_distributed_blast -s 10.0.0 -w workers  'blastn -task blastn-short -db my_db.fasta -query ~/seqs/sample.fasta -outfmt 6 -out output_file'

Then you only need to submit your job with mnsubmit

mnsubmit sample_work_moab.sh

LICENSE:

(The MIT License)

Copyright © 2011 Dario Guerrero

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the ‘Software’), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED ‘AS IS’, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.