Download both the source and the examples tar files into the same parent directory. Then, from the commandline, untar the source using the following command:
$> tar -xvzf mobios-v0.9-library.tar.gz
Once the source has been untarred, you must build the mobios.jar file:
$> cd mobios-v0.9-library/
$> ant jar
For more building instructions, including how to build the javadocs, see the readme located at mobios-v0.9-library/README.
Now go back to the parent directory and untar the examples directory:
$> cd ../
$> tar -xvzf mobios-v0.9-examples.tar.gz
$> cd mobios-v0.9-examples/
$> ls
Inside of mobios-v0.9-examples/ you should see the following subdirectories:
dna/
msms/
peptide/
vector/
The contents of each subdirectory are similar. Each contains a sample dataset, a shell script to build the index (build.sh), a shell script to query the index (query.sh), and in some cases a separate query dataset.
As an example, let's look at the dna directory:
$> cd dna/
The example dataset for dna is called data.fasta. The dataset for each type is required to be in a specific format; for dna, data must be in the FASTA format. For more information on what FASTA formatting looks like, as well as the formats accepted by MoBIoS for each type, click here.
To build an index over the dna dataset, type the following:
$> chmod +x build.sh
$> ./build.sh
build.sh contains one java command:
$> java -Xmx512M -cp ../../mobios-v0.9-library/build/mobios-v0.9.jar mobios.app.BuildVPIndex -t dna -d ../ -i data.fasta -o dna_11_100000 -p 2 -s 100000 -frag 11 -b 1
As you can see, build.sh calls the main bulkload interface to the MoBIoS library, BuildVPIndex. For more information on the options available when building an index, click here.
to query the index you have built:
$> chmod +x query.sh
$> ./query.sh
query.sh calls the main interface to the MoBIoS library, QueryVPIndex. For more information on the options available when querying an index, click here.
The results are saved in query.fasta.res.
Instructions for the other query sets are similar. If you have any problems building or querying an index over a specific data set, please send an email to willard AT cs PUNTO utexas PUNTO edu.
