wiki:ServerAdministration

Proteios SE server administration

Some configuration of the Proteios SE server is needed to enable all features. Furthermore, the administrator also needs to create user accounts and activate plug-ins, see the administration part of the user guide.

Tomcat memory settings

Tomcat by defaults run with little memory allocated to the Java Virtual Machine. Some Proteios SE plug-ins will require more memory, as will multiple concurrent users. It is thus recommended that you change the memory allocation to at least 512Mb. Depending on Tomcat version and base system, this can be done in different ways. Basically you'd like to set the environment variable JAVA_OPTS for tomcat to -Xmx512m (or higher).

  • On a SuSE Linux 11.x system with tomcat6 installed from YAST, you can edit JAVA_OPTS in /usr/share/tomcat6/conf/tomcat6.conf (10.x system and tomcat55 /srv/www/tomcat55/base/conf/tomcat55.conf).
  • If running Tomcat as a Windows service you can access the Java memory settings by the Monitor Tomcat tray icon.
  • Also see: Tomcat wiki.

Web server security

If you have Internet access to your Proteios SE server, it is advisable to use SSL encryptation of the connection, since passwords and settings are otherwise sent without encryptation. This is discussed here. Also see ssl-howto for Tomcat.

FTP Server

The integrated Proteios SE ftp server needs to be started separately, see.

Configuration of Proteios SE Access to External Programs

Proteios SE supports use of some external programs for processing data files. The benefit of running the analysis from Proteios SE is that several data files may be selected for an analysis using the same parameters, and the result files will be automatically uploaded to Proteios SE. Some external programs are accessed via a web site, while others are typically installed on a local server. Proteios SE configuration settings for external programs are stored in text files named *.properties, stored in directory WEB-INF/classes/ in your Proteios SE installation. Template files for the configuration files are stored in the same directory with names ending in .properties.in. These files contain information on the available parameters.

Search Engine Configuration - General

There are several search engines that can be accessed directly from Proteios SE. The server administrator needs to edit the configuration files of these to point to the right URLs. Furthermore, for the Proteios SE results combination of multiple search engines, exactly the same databases need to be installed for the different search engines, with a decoy (random/reverse) part that has a specific prefix for all the random entries. Matrix Science provides a free script to generate such a database. Here you can download a modified script which will name modified IPI:IPI entries IPI:IPRNDx.x or IPI:IPREVx.x for easy parsing of accession numbers. Other entries will have a ###RND### or ###REV### prefix. The script should be run with the --append option so that the decoy database is added at the end of the existing database. If you plan to do PMF searches or 'no enzyme' searches, the --random option is preferable. If you use local reference (.dat) files for Mascot IPI databases, the .dat will also need to be expanded using this script

X!Tandem configuration

Locate the Proteios X!Tandem search properties file xtandem.properties, which can be found under WEB-INF/classes in your installation. If not existing, locate the Proteios X!Tandem search properties file template xtandem.properties.in, and copy it to a file named xtandem.properties in the same directory.

Edit the xtandem.properties file by setting the value of the following parameters (more information and examples can be found in the file):

  1. Set the value of xtandem.gpm.server.url to the URL for the GPM web site to use for the search.
  2. Set the value of xtandem.gpm.result.filename.prefix to the prefix used for result files.
  3. Set the value of xtandem.gpm.server.timediff.hours to the time difference in hours of a GPM server in another time zone.
  4. Set the value of xtandem.gpm.server.timediff.correction.minutes to the difference in system clock settings.
  5. (Proteios SE 2.16.0 and later) If parameter xtandem.local.disabled is set to "yes", the X!Tandem functionality in Proteios SE will be disabled. This is intended to be used when X!Tandem is not configured, and prevents the functionality from being used with an error as result. When X!Tandem is properly configured, parameter xtandem.local.disabled should be set to "no".

The other settings can normally be used with their default values. For a local GPM install the commented settings in the xtandem.properties file can be used. If you are not sure about the GPM result filename prefix, just "GPM" should work in most cases. Otherwise, run a search through the web interface and check how the result is named.

OMSSA configuration

Install OMSSA according to the instructions at OMSSA download pages. Process your fasta databases using formatdb from the Blast distribution. The output files from formatdb should all be located in the same directory. Locate the Proteios OMSSA search properties file omssa.properties. If not existing, locate the Proteios OMSSA search properties file template omssa.properties.in, and copy it to a file named omssa.properties in the same directory.

Edit the omssa.properties file by setting the value of the following parameters (more information and examples can be found in the file):

  1. Set the value of omssa.local.install.path to the path for the locally installed OMSSA search engine.
  2. Set the value of omssa.local.program.name to the name of the OMSSA search program (normally "omssacl").
  3. Set the value of omssa.local.database.directory.path to the path of the local directory, where the sequence libraries (databases) are installed.
  4. Set the value of omssa.local.input.basename to base name of the created OMSSA input files (a time stamp will be added to make the final name). The default choice is "omssa_input.xml".
  5. (Proteios SE 2.16.0) If parameter omssa.local.disabled is set to "yes", the OMSSA functionality in Proteios SE will be disabled. This is intended to be used when OMSSA is not configured, and prevents the functionality from being used with an error as result. When OMSSA is properly configured, parameter omssa.local.disabled should be set to "no".

The settings above concern a locally installed OMSSA search engine, which is currently supported.

Mascot configuration

Mascot searches can be conducted in batch from Proteios SE similarily to X!tandem searches, and search results from Mascot Daemon searches can be retrieved in batch. For this to work, you need to edit the mascot server settings in the file mascot.properties, which can be found under WEB-INF/classes in your Proteios SE installation. After editing the file you need to restart Tomcat.

  1. (Proteios SE 2.16.0 and later) If parameter mascot.local.disabled is set to "yes", the Mascot functionality in Proteios SE will be disabled. This is intended to be used when Mascot is not configured, and prevents the functionality from being used with an error as result. When Mascot is properly configured, parameter mascot.local.disabled should be set to "no".

msInspect feature detection configuration

Proteios SE supports msInspect feature detection, when installed as a JAR file available from http://proteomics.fhcrc.org/CPL/msinspect/index.html. A release or nightly build of msInspect newer than March 2010 should be used for full mzML functionality. Locate the Proteios SE msInspect search properties file msinspect.properties. If not existing, locate the Proteios SE properties file template msinspect.properties.in, and copy it to a file named msinspect.properties in the same directory.

Edit the msinspect.properties file by setting the value of the following parameters (more information and examples can be found in the file):

  1. Set the value of msinspect.local.install.path to the path for the directory in which the msInspect JAR file is installed.
  2. Set the value of msinspect.local.program.name to the name of the installed msInspect JAR file (normally of type "viewerApp*.jar", where '*' represents an optional time stamp and serial number).
  3. Set the value of msinspect.memory_in_megabytes to the memory in MB to use for the Java Virtual Machine, when running the msInspect program (at least 512 MB is recommended).
  4. (Proteios SE 2.16.0) If parameter msinspect.local.disabled is set to "yes", the msInspect functionality in Proteios SE will be disabled. This is intended to be used when msInspect is not locally installed, and prevents the functionality from being used with an error as result. When msInspect is locally installed and configured, parameter msinspect.local.disabled should be set to "no".

OpenMS feature detection configuration

Proteios SE supports OpenMS feature detection using programs PeakPicker and FeatureFinder, separately or in a pipeline. The OpenMS package can be obtained from http://open-ms.sourceforge.net/openms/, and is installed locally. A release newer or equal to OpenMS 1.7 should be used for full mzML functionality. Locate the Proteios SE OpenMS search properties file openms.properties. If not existing, locate the Proteios SE properties file template openms.properties.in, and copy it to a file named openms.properties in the same directory.

Edit the openms.properties file by setting the value of the following parameters (more information and examples can be found in the file):

  1. Set the value of openms.local.install.path to the path for the directory in which the OpenMS programs PeakPicker and FeatureFinder are installed.
  2. Set the value of openms.local.program.peak_picker.name to the name of the installed PeakPicker program (normally just "PeakPicker" on Unix/Linux systems, and "PeakPicker.exe" on Microsoft Windows).
  3. Set the value of openms.local.program.feature_finder.name to the name of the installed FeatureFinder program (normally just "FeatureFinder" on Unix/Linux systems, and "FeatureFinder.exe" on Microsoft Windows).
  4. (Proteios SE 2.17 and later) If parameter openms.local.disabled is set to "yes", the OpenMS functionality in Proteios SE will be disabled. This is intended to be used when OpenMS is not locally installed, and prevents the functionality from being used with an error as result. When OpenMS is locally installed and configured, parameter openms.local.disabled should be set to "no".

Note on Installing OpenMS on Unix/Linux Systems

The OpenMS programs require that some environment variables are updated with paths to used libraries, specifically variable LD_LIBRARY_PATH. For the OpenMS programs to work with Proteios SE, the environment in the terminal command window from which the Tomcat server is started from its startup.sh script, must fulfill these requirement. This is most easily tested by giving the run command for program PeaKPicker or FeatureFinder in this terminal command window. If the program returns a list of available options, the environment variables are correctly set, while if an error message is returned, the environment variables must be updated. For what environment variables to update, and with what information, please see the OpenMS documentation.

PIKE configuration

Proteios SE can access a PIKE web site to fetch information for input protein list files, and upload the result files. The PIKE server settings are stored in file pike.properties, which can be found under WEB-INF/classes in your Proteios SE installation. The default settings can normally be used, but the file may be edited if you want to access another PIKE web site. After editing the file you need to restart Tomcat.

Retrieval of remote files

Remote files can be registered by their URI and used in Proteios as if they were located on the Proteios server. Click here to read about how to configure your server to access files via https using certificates (needed for BILS).

Last modified 5 years ago Last modified on Jan 10, 2013, 9:11:01 AM

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