=======Maker========

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: [[http://www.yandell-lab.org/software/maker.html|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.

=====Running Maker======

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 [[http://gmod.org/wiki/MAKER_Tutorial|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.