Maker is a genome annotation pipeline that we are intending to use once we have a well put together assembly. It's homepage can be found here: Yandell Lab.

Maker has been installed on CampusRocks in /campusdata/jdhouser/maker/ and a symlink has been placed in /campusdata/BME235/bin/ so that it can be run from there. Running Maker requires modifying your bash profile with the following:

export ZOE=“/campusdata/jdhouser/snap/Zoe”

Maker also supports installing a number of optional programs to be used in its pipeline. One of them, Augustus, requires you add:

export AUGUSTUS_CONFIG_PATH=“where_augustus_is/config”

to your bash profile as well.

Maker is run via options and exec files. You can generate these files in your current directory by using the command:

maker -CTL

From there, you can simply run maker in the directory with the control files. Step by step instructions on how to run Maker can be found on this wiki article.

As of this writing, given that we do not have an assembly worth running maker on and the limited nature of time remaining in the quarter, I have not run maker on any of the assemblies so the above wiki link will be a better reference than I am.