Installation: Mac OS X app

The Mac OS X bundle is an easy way to use SeqPlots for Mac OS X users. It contains all R binaries and packages that SeqPlots depends on. Additionally, the reference sequences for Caenorhabditis elegans is included. The sequences for other popular model organisms can be downloaded using a graphical user interface.

System requirements

• Mac OS X Snow Leopard (10.6) or higher

Installation

1. Downaload the installation disk image from http://bitbucket.org/przemol/seqplots/downloads
2. Double-click on DMG file to mount the image

3. Drag and drop SeqPlots.app to applications

   

Usage

After starting SeqPlots the welcome screen displays the software version, the currently installed genomes and the data folder location.

This screen allows you to set up following options:

• Change your data location folder (by default your home directory will be used)

• Install new genomes (requires internet connection). The correct genome packages need to be installed before before uploading files for plotting. A full list of supported genomes is available here: http://www.bioconductor.org/packages/release/BiocViews.html#___BSgenome

  

Press the START button to initiate SeqPlots. If initiation was successful the user interface should open in your default web browser.

For further usage please refer to quick start guide or specific chapters of documentation.

The window in the background allows you to assess if SeqPlots is running properly and exit the application at any moment.

The "moving" animation progress bar indicates that SeqPlots is running. Press "Cancel" to stop it. Pressing "Details" will reveal a small text window that displays diagnostic and error messages.

Package content

• Platypus (http://www.sveinbjorn.org/platypus) wrapper
• R (http://www.r-project.org/) branch 3.1 for Snow leopard (http://r.research.att.com/snowleopard/R-3.1-branch/R-3.1-branch-snowleopard-sa-x86_64.tar.gz)
• SeqPlots dependency packages (including Shiny, rtracklayer and BSgenome)
• Full genome sequences for Caenorhabditis elegans (UCSC version ce10) - BSgenome.Celegans.UCSC.ce10 R package
• SeqPlots package