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=======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.

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archive/maker.1433357905.txt.gz · Last modified: 2015/06/03 18:58 by jdhouser