Application Name
Blast Binary
Summary
- Name: Blast Binary
- Contact Person: support-compss@bsc.es
- Access Level: public
- License Agreement: Apache2
- Platform: COMPSs
- Repository: Blast Binary
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
BINARY VERSION
Execution instructions
Usage: export BLAST_BINARY=<blast_binary> runcompss blast.Blast <debug> <database> <sequences> <#fragments> <tmpDir> <outputFile> <extra_cmd_args> where:
- - debug: Set the debug mode on
- - 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
export BLAST_BINARY=/home/user/workspace/blast/binary/blastall runcompss blast.Blast true /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/blastbinary/; javac src/main/java/blastbinary/*.java cd src/main/java/; jar cf blastbinary.jar blast/ cd ../../../; mv src/main/java/blastbinary.jar jar/
Option 2: Maven
cd ~/workspace_java/blastbinary/ mvn clean package