Application Name

Blast

Summary

• Name: Blast
• Contact Person: support-compss@bsc.es
• Access Level: public
• License Agreement: Apache2
• Platform: COMPSs
• Repository: ​Blast

Description

BLAST (Basic Local Alignment Search Tool) is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or nucleotides of DNA sequences. BLAST enables a researcher to compare a query sequence with a library or database of sequences, and identify sequences that resemble the query sequence above a certain threshold.

The COMPSs application contains three main blocks:

– Split: the query sequences file is splitted in N fragments.

– Alignment: each sequence fragment is compared against the database by the blast binary.

• Assembly: assembly process combines all intermediate files into a single result file.

Versions

There are two versions of the BLAST application, varying on how the merge operation is performed

Version 1

2-by-2, the results of the Alignment tasks are merged 2 by 2

Version 2

All-to-One, this version processes the merge operation in one final step

Execution instructions

Usage: runcompss blast.Blast <debug> <binary> <database> <sequences> <#fragments> <tmpdir> <output> <cmd_args>

where:

• - debug: Set the debug mode on
• - binary: Blast binary location
• - database: Database Name
• - sequences: Input sequences path
• - #fragments: Fragments number
• - tmpdir: Temporary directory
• - output: Output file
• - cmd_args: Command line Arguments of the Blast binary

Execution Example

runcompss blast.Blast true /home/user/workspace/blast/binary/blastall /sharedDisk/blast/databases/swissprot/swissprot /sharedDisk/blast/sequences/sargasso_test.fasta 4 /tmp/ /home/user/out.txt

Build

Option 1: Native java

cd ~/workspace_java/blast/; javac src/main/java/blast/*.java cd src/main/java/; jar cf blast.jar blast/ cd ../../../; mv src/main/java/blast.jar jar/

Option 2: Maven

cd ~/workspace_java/blast/ mvn clean package