Changes between Initial Version and Version 1 of application_pages/apps/java/blast

Timestamp:

10/26/15 09:33:28 (9 years ago)

Author:

trac

Comment:

--

application_pages/apps/java/blast

@@ +1 @@
+[[PageOutline]]
+
+= Application Name =
+
+Blast
+
+= Summary =
+
+* '''Name''': {{{Blast}}}
+* '''Contact Person''': {{{support-compss@bsc.es}}}
+* '''Access Level''': {{{public}}}
+* '''License Agreement''': {{{Apache2}}}
+* '''Platform''': {{{COMPSs}}}
+* '''Repository''': [[https://compss.bsc.es/svn/bar/apps/java/blast|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