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Welcome to project pview-cli

Goal

The pview tool created by Zia Khan is a very fast and useful tool for processing proteomics data (pview = Princeton LC-MS/MS Data Viewer and Analyzer, see compbio.cs.princeton.edu/pview). At the moment, pview has a graphical user interface which makes it hard to integrate in an automated pipeline. The pview-cli project was started to add command line access to pview, especially for use in systems such as Galaxy (an open, web-based platform for computational biomedical research, see wiki.g2.bx.psu.edu).

The self-imposed criteria for this project are:

  • 100% command line based operation, with input and output files as options.
  • No dependencies on Qt (the platform independent GUI library that is used by pview, see qt.nokia.com).
    • This will now be accomplished by static building, see instructions on how to build Qt statically below
  • No, or minimal changes to the original code base.

First (technical) steps

A couple of things have been done:

  • A separate Qt Creator project has been made, pview-cli.pro including the files of the original code base, excluding MSWin.cpp/h and MSMSWin.cpp/h and explicitly excluding Qt as a library.
  • Two additional files (anyoption.cpp/h) have been included in the pview-cli project, for simple command-line parsing.

Plans - near future

The pview-cli executable that can be built by compiling this new project, should handle these inputs:

  • A collection of mzXML files as raw data.
  • An experiment-design file, containing the function of each raw file (experimental, replicas, etc.; the regular version of pview scans a folder structure, which makes it harder to integrate with some frameworks).
  • A settings.xml file containing parameters for the analysis.
  • FASTA files for database searching.
  • pepXML files as a result from searching for peptides in other databases.

For the integration of pview-cli in Galaxy:

  • A Galaxy front-end must be created, preferentially easing the creation of the settings.xml file and the experiment-design file.

Plans - further future

Mailing lists

This project provides the following mailing lists:

static Qt library

Qt source code can be downloaded from the Qt web site http://qt.nokia.com/downloads.

the following dependencies should be met (names based on XUbuntu 11.10)

  libexpat1-dev
  fontconfig1-dev

The following tools are needed:

   g++
   build-essential

in the extracted qt source folder the following commands should be issued:

  make clean
  ./configure -static -stl -nomake demos -nomake examples
  make
  sudo make install

January 31th

JanuaryThirtyFirst

Source access

If available, anonymous readonly subversion access works as follows:

  svn co https://trac.nbic.nl/svn/pview-cli pview-cli

If you have any problems checking out the source, please send an e-mail to the pview-cli-users mailing list. Write access is only available to registered developers.

You can become a developer by registering yourself if you haven't already done so, and requesting write access on the pview-cli-users mailing list.

Starting Points

Other NBIC software projects

All active NBIC software projects can be accessed from the project index.

Last modified 10 years ago Last modified on Jan 31, 2012, 10:46:30 AM