WebHERV

WebHERV front-end with the key-value store DRUMS.

WebHERV (http://calypso.informatik.uni-halle.de/WebHERV/) is a web GUI that enables the user to access HERV (Human endogenous retrovirus)-like elements or any other genome positions stored in the underlying highly optimized key-value store DRUMS (https://github.com/mgledi/DRUMS).

The following subsections describe how to set up the WebHERV front-end as well as the back-end with HERVs but it can be customized to any other type of genomic positions.

1. Determine HERV-like sequences

To determine the HERV-like sequences in the human genome, we used the standalone version of BLAST (Basic Local Alignment Search Tool).

The latest version of BLAST can be downloaded from ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/.

The current human genome can be downloaded from ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/.

The program blastn with the output option -outfmt 6 was used to search for more HERV-like sequences in the human genome using known HERV sequences. For the first version of WebHERV we used HERV coordinates from a published data base (Villesen et al. (2004) Retrovirology 11,1-32).

  ./blastn -query hervSequences.fa -db ./human_genome_dir -out blast_output.out -outfmt 6 -evalue 1e-10

1.1 Other genomic positions

Similar to the HERV-like sequences any other type of sequences or reference genomes can be used to determine genomic positional information.

2. WebHERV sources

Download the WebHERV source from GitHub:

 git clone https://github.com/etsnok/WebHERV.git

After downloading, change to the WebHERV directory.

cd ./WebHERV/

This directory contains all the neccessary files to set up and compile the WebHERV webapp.

3. Setup DRUMS store and WebHERV

The directory WebContent/WEB-INF/ contains all configuration files that are needed to set up your own WebHERV.

3.1 DRUMS setup

To manage the high number of BLAST hits we use the highly optimized key-value store DRUMS.

To set up a DRUMS DB, set the location for the DRUMS store in the WebContent/WEB-INF/drums.properties directory.

  DATABASE_DIRECTORY=/path/to/drums/db/your_db/`

your_db is the directory where the DRUMS DB will be stored (or is stored if it already exists).

NOTE: The WebHERV is designed to hold multiple DRUMS DBs. Therefore you can create additional DRUMS DBs next to your_db e.g.: /path/to/drums/db/your_db_2/

3.2 WebHERV setup

To register your DRUMS DB for the WebHERV front-end you need to edit the following two configuration files:

web.xml

First, to enable accessing the file system directory containing the DRUMS directories (/path/to/drums/db/) in WebContent/WEB-INF/web.xml you need to set the following parameter:

<context-param>
	<param-name>drumsDatabasesDir</param-name>
	<param-value>/path/to/drums/db</param-value>
</context-param>

Otherwise the WebHERV would have not the rights to read the file system.

NOTE: the path is the parent directory of your_db so that other directories like your_db_2 are also accessible.

drums.properties

Second, to register your DRUMS DBs in the WebHERV front end you need to edit the WebContent/WEB-INF/drums.properties file. There you need to set the drums.directory.path to the directory containing your DRUMS DBs. The individual databases need to be registered by drums.databases.hervs.your_db.

  drums.directory.path="/path/to/drums/db"

  # hg19 drums database
  drums.databases.hervs.your_db.id=your_db
  drums.databases.hervs.your_db.dir=your_db
  drums.databases.hervs.your_db.genome=hg19

  # hg18 drums database
  drums.databases.hervs.your_db_2.id=your_db_2
  drums.databases.hervs.your_db_2.dir=your_db_2
  drums.databases.hervs.your_db_2.genome=hg18

NOTE: the parameter genome must be set to either hg18 or hg19.

3.3 WebHERV packaging

After setting up the WebHERV and DRUMS configurations you can package your WebHERV by running:

mvn package

in the ./WebHERV/ directory.

This will produce the files WebHERV-X.X.X.war and a WebHERV-X.X.X.jar in the ./target/ directory.

4. Fill DRUMS database

After packaging the WebHERV you can use the WebHERV-X.X.X.jar to create and fill your DRUMS DB with data.

Use the java program org.kkruse.webherv.upload.WebHERVWriter to create the DRUMS store in consideration of your drums.properties file.

Creating the DRUMS store:

java -jar ./target/WebHERV-0.0.1.jar ./WebContent/WEB-INF/drums.properties 0

After this you can fill the created DRUMS store with your BLAST output data (blast_output.out) by running:

java -jar ./target/WebHERV-0.0.1.jar ./WebContent/WEB-INF/drums.properties 1 path/to/your/blast_output.out

5. Fill probe sets

Currently, the WebHERV accesses a simple SQLite database holding the genomic positions for the Affymetrix Human Exon 1.0 ST arrays hg18 and hg19 stored in the database file.

6. Run WebHERV server

Finally, you are able to run the web-server by deploying it to server (e.g. tomcat) or starting a local Jetty instance.

6.1 Server

You can take the .war file containing the front end with all properties and deploy it in the webapps directory of your server e.g. tomcat.  

The front-end will be accessible by something like: http://your_server_url/WebHERV/

6.1 Local Jetty instance

Or you can start a local Jetty server instance from WebHERV via:

java -jar target/dependency/jetty-runner.jar target/*.war

and in your browser enter the following URL: http://localhost:8080/