GEP Installation Package

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In order to maximize the number of faculty that can participate in the partnership, most of the tutorials we have developed are completely web-based. However, faculty and students who wish to participate in the GEP sequence improvement project must have access to computers with the Consed package installed.

Installing Software

You can update/install Consed through one of the three mechanisms listed below:

  1. Install and run on a Mac (Mac OS 10.6 or higher is required to run the current version of Consed). To follow this path, see Installation on Mac systems below.
  2. Install on a UNIX or Linux-based system. Installation requirements vary by system; contact Chris or Wilson if you want to explore this option
  3. Run Consed using a Live CD or inside a virtual machine. This can be done on most of the Mac, Linux, or Windows based systems using the free software VirtualBox. This is probably the best option for those schools wishing to do sequence improvement in a Windows-based computer lab.

Installation on Mac systems

Minimum System Requirements for Sequence Improvement:

  1. Mac OS 10.6 or higher
  2. 512 MB of RAM
  3. X11 (installed by default in 10.6 and 10.7; available for 10.8 - 10.12)


Instructions for installation on Mac OS X (OS 10.8 - 10.12) is available as a Word document.

If possible, please install version 2.7.9 of XQuartz as described in the installation instructions. Consed is currently incompatible with more recent versions of X11 (i.e. XQuartz 2.7.10 and 2.7.11).

Please contact Wilson if you are in a computer lab where a more recent version of XQuartz is already installed. We have developed an unofficial patch for Consed so that it will run on XQuartz 2.7.10 and above.

Project Specific Data Files

If you need to update any of the project specific files, they are available from these links:

  1. phredpar.dat,
  2. tagTypes.txt
  3. vector.seq.

The above must be placed in /usr/local/genome/lib/. For any of the Drosophila projects, the files below should be placed in /usr/local/genome/lib/screenLibs/. If your copy of consed is installed in a location other than the default all these files should be placed in lib/screenLib of the directory determined by the value of the environment variable $CONSED_HOME instead of the directories mentioned above.

  1. primerCloneScreen.seq
  2. primerSubcloneScreen.seq
  3. singleVectorForRestrictionDigest.fasta
  4. repeats.fasta

GEP Live CD and Virtual Machines

Besides installing Consed on a computer running Mac OS 10.6 or above, you can also run Consed using the GEP Live CD. The GEP Live CD enables you to run Consed on all three major platforms (MS Windows, Mac OS X, and Linux).

The Live CD can be used in many different configurations and settings: as a standalone bootable Live CD, a bootable Live CD inside a virtual machine, or as a virtual machine in VirtualBox. The GEP Live CD ISO image and the GEP Live CD virtual appliance is available for download on the Projects Under Development page on the GEP web site.

The GEP Live CD allows you to experiment with the Consed software without making permanent changes to your computer. You can either burn the ISO image to a CD or mount the ISO image as a disk inside a virtual machine. Note that most virtualization software (e.g. VirtualBox, VMWare, Parallels, Virtual PC) support mounting ISO disk images. Hence the Live CD should work on many virtualization platforms with only minor changes.

In addition to running Consed as part of a Live CD, you can also run Consed as part of a virtual machine in VirtualBox. We decided to use VirtualBox because it runs on all three major platforms (Windows, Mac OS X, and Linux) and it is free for academic and personal use. However, the GEP virtual machine is distributed as an Open Virtualization Appliance (OVA package) so that it is compatible with most virtualization platforms.

Please refer to the GEP Live CD User Guide for additional instructions on how to install and configure the GEP Live CD and the GEP Live CD virtual appliance.