| 1 | [[PageOutline]] |
| 2 | |
| 3 | = Application Name = |
| 4 | |
| 5 | Blast Allone |
| 6 | |
| 7 | = Summary = |
| 8 | |
| 9 | * '''Name''': {{{Blast Allone}}} |
| 10 | * '''Contact Person''': {{{support-compss@bsc.es}}} |
| 11 | * '''Access Level''': {{{public}}} |
| 12 | * '''License Agreement''': {{{Apache2}}} |
| 13 | * '''Platform''': {{{COMPSs}}} |
| 14 | * '''Repository''': [[https://compss.bsc.es/svn/bar/apps/java/blastallone|Blast Allone]] |
| 15 | |
| 16 | |
| 17 | == Description == |
| 18 | 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. |
| 19 | |
| 20 | The COMPSs application contains three main blocks: |
| 21 | |
| 22 | – Split: the query sequences file is splitted in N fragments. |
| 23 | |
| 24 | – Alignment: each sequence fragment is compared against the database by the blast binary. |
| 25 | |
| 26 | - Assembly: assembly process combines all intermediate files into a single result file. |
| 27 | |
| 28 | |
| 29 | == Versions == |
| 30 | There are two versions of the BLAST application, varying on how the merge operation is performed |
| 31 | === Version 1 === |
| 32 | ''2-by-2'', the results of the Alignment tasks are merged 2 by 2 |
| 33 | === Version 2 === |
| 34 | ''All-to-One'', this version processes the merge operation in one final step |
| 35 | |
| 36 | |
| 37 | == Execution instructions == |
| 38 | Usage: |
| 39 | runcompss blast.Blast <debug> <binary> <database> <sequences> <#fragments> <tmpdir> <output> <cmd_args> |
| 40 | |
| 41 | where: |
| 42 | * - debug: Set the debug mode on |
| 43 | * - binary: Blast binary location |
| 44 | * - database: Database Name |
| 45 | * - sequences: Input sequences path |
| 46 | * - #fragments: Fragments number |
| 47 | * - tmpdir: Temporary directory |
| 48 | * - output: Output file |
| 49 | * - cmd_args: Command line Arguments of the Blast binary |
| 50 | |
| 51 | == Execution Example == |
| 52 | 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 |
| 53 | |
| 54 | |
| 55 | == Build == |
| 56 | === Option 1: Native java === |
| 57 | cd ~/workspace_java/blastallone/; javac src/main/java/blast/*.java |
| 58 | cd src/main/java/; jar cf blastallone.jar blast/ |
| 59 | cd ../../../; mv src/main/java/blastallone.jar jar/ |
| 60 | |
| 61 | === Option 2: Maven === |
| 62 | cd ~/workspace_java/blastallone/ |
| 63 | mvn clean package |