What is Javamage
Javamage is the Java part of Merlin
Merlin consists of ...
- Front-End: This is how users can interact with Merlin inputs and outputs
- Server : This handles simple GET and POST requests made by the Front End. The server then uses Javamage to get run optimization
- Javamage : This is a Java package for performing Merlin Analysis on the package
How to use Javamage
See the javadoc for a more detailed explanation of how everything works.
Setup and Requirements
Merlin has the following Java based requirements. These are .jar files that can be found in the
- BioJava 3.0 [Sequenced, Alignment, Core]
- Javaplot [A plotting library for anaylsis]
Merlin has requires the follow EXTERNAL dependencies
makeblastdb: , comes with NCBI Blast+ Standalone
blastn: , comes with NCBI Blast+ Standalone
MFOLD: This requires UNAFOLD, available at
BioPython: Version 1.65 or later. Available at
To configure javamage to find these binaries, write down in the config.txt file found in the working directory the process name followed by the path to the binary
You can use the
which command to find out where these binaries live.
Below is a sample config.txt entry
makeblastdb /usr/local/ncbi/blast/bin/makeblastdb blastn /usr/local/ncbi/blast/bin/blastn MFOLD /usr/local/bin/hybrid-ss-min
ensure that you follow the order of this format
Look at the
javamage/test/Unit/Merlin.java file to get an example of how to use java ma
Open the file and change the 'merlin test dir' string to link to YOUR wordking directory folder.
After this setup the correct file names. These files should be in the working directory folder
genomeFileName: A Fast file of the genome
targetFileName: An optMAGE target File name
parametersFileNamie: An optMAGE parameter File
Using these 4 parameters we create a new Merlin object
We enable and disable certain procedures like plotting.
We can set Switches, like the BLAST Scoring method, with the
The finally the
.optimize() method will run the Merlin Optimization analysis.
Then on the last commented line is allows you to compare merlin results to optmage results that are provided in an OUTOligos file in the resources folder)
Java Analysis Tool with optMAGEv0.9 Created by Samir Ahmed 2011-2012
Javamage is available under the BSD 3-Clause License (http://opensource.org/licenses/BSD-3-Clause)