Welcome to project pview-cli
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
- pview should be able to read mzML (see psidev.info/index.php?q=node/303) and mzIdentML (see psidev.info/index.php?q=node/454) files.
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)
The following tools are needed:
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
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.
- TracGuide -- Built-in Documentation
- TitleIndex -- A complete list of local wiki pages.
- Trac FAQ -- Frequently Asked Questions
Other NBIC software projects
All active NBIC software projects can be accessed from the project index.