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:

  •  pview-cli-users: a list intended for general discussion on the project.
  •  pview-cli-commits: a list that receives source code commit messages.
  •  pview-cli-devel: a list intended for discussion among developers (subscription is restricted to registered developers).

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

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