[[PageOutline]]

= Application Name =

Blast Blanks

= Summary =

* '''Name''': {{{Blast Blanks}}}
* '''Contact Person''': {{{support-compss@bsc.es}}}
* '''Access Level''': {{{public}}}
* '''License Agreement''': {{{Apache2}}}
* '''Platform''': {{{COMPSs}}}
* '''Repository''': [[https://compss.bsc.es/svn/bar/apps/java/blastblanks|Blast Blanks]]


 == 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.

Only for tutorial purposes.


== 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/blastblanks/; javac src/main/java/blast/*.java
cd src/main/java/; jar cf blastblanks.jar blast/
cd ../../../; mv src/main/java/blastblanks.jar jar/

=== Option 2: Maven ===
cd ~/workspace_java/blastblanks/
mvn clean package