Installation

There are three ways to install RNAseqViewer. Binaries are provided for some configurations of Windows and Linux. If they don’t work, you can choose the third and installing from the source.

Windows Installer

If you use Windows, the easiest way to install RNAseqViewer may be to download (see the download page) and run the Windows Installer. You can choose some options like the path where to install the program. When installation is finished, you can start using RNAseqViewer.

The Windows Installer was tested on Windows 7 SP1 and Windows XP pro SP3.

Linux Binaries

Using Linux binaries can be a quick way to install RNAseqViewer on some Linux distributions. Just download (see the download page) and uncompress the binaries. You can directly run the program RNAseqViewer:

wget http://bioinfo.au.tsinghua.edu.cn/software/RNAseqViewer/download/X.X.X/RNAseqViewer-X.X.X-linux-i686.tar.gz
tar -xf RNAseqViewer-X.X.X-linux-i686.tar.gz
cd RNAseqViewer-X.X.X-linux-i686/
./RNAseqViewer

where X.X.X should be replaced by the latest version number (e.g. 0.7.2).

Tested on Ubuntu 12.04 and OpenSUSE 12.2.

There is a specific version of the binaries for Debian (see the download page):

wget http://bioinfo.au.tsinghua.edu.cn/software/RNAseqViewer/download/X.X.X/RNAseqViewer-X.X.X-debian-i686.tar.gz
tar -xf RNAseqViewer-X.X.X-debian-i686.tar.gz
cd RNAseqViewer-X.X.X-debian-i686/
./RNAseqViewer

Install from source

The last installation method is general purpose and should work on most systems.

You should first install Python 3 and PySide (only core, gui and svg packages are needed). If you want to visualize SAM/BAM files, you should also install Samtools and if your plan to visualize Tabix-compressed GTF files, you should also install Tabix. These programs may be present in your Linux distribution’s default package repository.

For example, on Debian, you should run:

apt-get install python3-all-dev python3-pyside samtools tabix

When you get these programs installed, you can download (see the download page) and uncompress the sources, and run RNAseqViewer.py with Python 3:

wget http://bioinfo.au.tsinghua.edu.cn/software/RNAseqViewer/download/X.X.X/RNAseqViewer-X.X.X.tar.gz
tar -xf RNAseqViewer-X.X.X.tar.gz
cd RNAseqViewer-X.X.X-linux-i686/
python3 RNAseqViewer.py

where X.X.X should be replaced by the latest version number (e.g. 0.7.2).

Tested on Windows 7 and Ubuntu 12.04, with Python 3.2, PySide 1.1.0, Samtools 0.1.12 and Tabix 0.2.5.