Spectral Networks - Installation guide

This page provides the details necessary to download, install and maintain the Spectral Networks package.

Main Topics

System Requirements

Currently, Spectral Networks is available for Linux x64 and x86 based systems. For distributed computing, Sun Grid Engine and PBS are supported.

Downloading

The Spectral Networks package download page can be found at:
http://usa.ucsd.edu:8080/projects/sps/jcanhita/Download/

Select the appropriate package and click in the corresponding link to download.

Installing

Unzip the Spectral Networks package to a directory <installation directory> (any directory of your choice). This directory should then containing the following directories:

  • sps/bin - Contains the binary executables
  • sps/cgi - Contains CGI scripts used by the program
  • sps/Doc - Documentation
  • sps/example - Test project

Web server

SPS is a command line tool that outputs reports in HTML format. Report pages may accessed using a web browser to render the HTML report files generated. These files should be made available by SPS using a web server such as Apache.
To enable interactivity in protein sequencing reports (see results documentation), there are several CGI scripts needed that should be present in the web server's configuration file:

  • <installation directory>/sps/cgi/specplot.cgi
  • <installation directory>/sps/cgi/contplot.cgi
  • <installation directory>/sps/cgi/spsReports.cgi

Additionally, the web server process should have write permission on project directory and on report generated files in order to allow sequence edits to be kept over time, and to allow the re-alignment procedure.

Configuration

The following changes should be made in the installed scripts:

  • Edit <installation directory>/cgi/spsReports.cgi at line 12. The line should be:
    • $ENV 'LD_LIBRARY_PATH' = “<installation directory>/sps/bin/libs”;
  • Edit <installation directory>/cgi/spsReports.cgi at line 8. The line should be:
    • $SPS_DIR = “<installation directory>/sps/”;
  • Edit <installation directory>/cgi/specplot.cgi at line 32. The line should be:
    • $ENV 'LD_LIBRARY_PATH' = “<installation directory>/sps/bin/libs”;
  • Edit <installation directory>/cgi/specplot.cgi at line 27. The line should be:
    • $TMP = “<TMP_DIRECTORY>”;
      where TMP_DIRECTORY is a directory in the file system where the server process has write permissions
  • Edit <installation directory>/cgi/specplot.cgi at line 28. The line should be:
    • $SPS_DIR = “<installation directory>/sps/>”;
  • Edit <installation directory>/cgi/contplot.cgi at line 32. The line should be:
    • $ENV 'LD_LIBRARY_PATH' = “<installation directory>/sps/bin/libs”;
  • Edit <installation directory>/cgi/contplot.cgi at line 27. The line should be:
    • $TMP = “<TMP_DIRECTORY>”;
      where TMP_DIRECTORY is a directory in the file system where the server process has write permissions
  • Edit <installation directory>/cgi/contplot.cgi at line 28. The line should be:
    • $SPS_DIR = “<installation directory>/sps/>”;

Testing the installation

In order to test the installation, a test project and data are included in the package, in the directory named 'example'. To test the installation, execute the following procedures:

  • cd to <installation directory>/sps/example
  • edit the sps.params file.
    • EXE_DIR should point to <installation directory>/sps/bin (should be an absolute path).
    • REPORT_DIR defines the output directory for report files, should be in the webserver path, allowing for report pages to be served by the webserver (e.g. Apache).
    • GRID_SGE_EXE_DIR DIR should point to where SGE binaries are located (qstat, qsub, etc.).
    • GRID_EXE_DIR should point to where SPS binaries (the same pointed by EXE_DIR) are seen on SGE.
    • SERVER *should point to the server’s CGI directory. Example:
    • SERVER=http://myserver.com/cgi-bin/*
  • run ../bin/main_specnets sps.params
  • From a webserver, open '<URL path in webserver>/index.html' which is located inside the specified report location directory, considering your webserver path specifications. The report initial page should be displayed.

Setting Spectral Networks to run on your grid

Spectral Networks assumes that all data files are copied from the head node to the compute nodes when submitting jobs, and that the directory structure is maintained under the compute nodes. This means that the paths for the same file under the head node and any of the compute nodes should be exactly the same. This is essential, as Spectral Networks relies on files to transfer information between the main process process and the child jobs that run on different nodes.

Several parameters related to the grid are used:

Parameter Values Default Description
GRID_TYPE sge / pbs sge Defines grid type
GRID_NUMNODES Integer   Defines the number of grid nodes that will be used by Spectral Networks
GRID_NUMCPUS integer   Defines the number of CPUs per node that will be used
GRID_EXE_DIR Path   Path to Spectral Netowrks executables directory
GRID_SGE_EXE_DIR Path   Path to grid related executables (qsub, qdel, etc.)
GRID_PARAMS String   Parameters to pass directly to the grid. Ex:
GRID_PARAMS="-l h_vmem=1G"
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