Customizing and Starting Metannogen

Metannogen requires Java: Java. The standard Java (Sun/Oracle), JRocket (Oracle), Java by IBM, Openjdk and the Macintosh Java are sufficient.

Web start

If the web browser is correctly configured, Metannogen can be Web-started by clicking the file metannogen.php . You may need to tell the web browser that files with the ending jnlp need to be processed with the application .../bin/javaws which is part of the Java system. The settings are usually imported from the default Web-browser. If this fails, metannogen will not be able to load data from the network. For debugging, the Web proxy setting can be checked in Metannogen.

For using Metannogen for a certain project, program parameters need to be adjusted. The members of the team may start metannogen by clicking a customized Web link such that Metannogen is properly configured for the specific project.

Metannogen is controled by program parameters. If Metannogen is web-started by clicking the web link metannogen.php, program parameters can be passed as web variables (POST or GET). This PHP script dynamically genereates a jnlp file for the program ../bin/javaws. The HTML code of the web form may look like:

        <form  action="http://www.bioinformatics.org/strap/metannogen/metannogen.php"  method="POST" >
          <input  type="hidden"  name="port"       value="10117"  >
          <input  type="hidden"  name="edtftp"     value="t" >
          <input  type="hidden"  name="networks"   value="KEGG RECON1 EHM" >
          ... more program options ... 
          <input  type="SUBMIT"  name="SUBMIT"     value="Run metannogen" >      
        </form>
      

Shell script

Alternatively the Java file metannogen.jar can be downloaded and started from the command line. This method is also more robust than Web-start. The minimal program line is

java -Xmx400M -jar metannogen.jar

Within an intranet the web proxy is specified by options of the java command. For example from the intranet of the medical school Charite in Berlin the following settings would be required for Metannogen to access the internet:

            
            java -Dhttp.proxyHost=realproxy.charite.de -Dhttp.proxyPort=888 -Dhttp.nonProxyHosts="www.charite.de|olli.charite.de"  ...            
          

For specific projects it is recommended to start Metannogen from a shell script. This shell script may be distributed to all team members such that Metannogen will be configured properly on all clients. On Linux, Mac, Solaris or Windows+Cygwin such shell script may look like:

            myWebProxy=-Dhttp.proxyHost=proxy.myInstitution.org
            myData=/home/me/metannogenData
            JAR=http://www.bioinformatics.org/strap/metannogen/metannogen.jar
            curl -O $JAR -z metannogen.jar || wget -N $JAR
            java $myWebProxy -Xmx400M -jar metannogen.jar \
            -port=10117 \
            -networks KEGG RECON1 EHMN \
            -dictionaryOfSpecies myData/myFile.txt 
          

The trailing back-slash characters allow continuation of a command in the next line. This back-slashes are the last character in the line. No white space must follow the trailing back-slashes.
_{Probably scripting will not work for MS-Windows because the length of the line exceeds the maximum. But it will work under Cygwin which can easily installed under Windows.}

Batch mode

With certain program parameters Metannogen runs non-interactively in batch mode to create an SBML file from a dataset file.

           
            java $myWebProxy -Xmx400M -jar metannogen.jar \
            -datasets $HOME/test/myDatasetFile.dataset  \
            -toSBML myOutputFile.sbml 
          

Deinstallation of Metannogen

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