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lecture_notes:04-20-2015 [2015/04/25 02:59] calef [Meraculous limitations] |
lecture_notes:04-20-2015 [2015/04/25 03:03] calef [User experience] |
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* Requires an array of other scripts in other languages | * Requires an array of other scripts in other languages | ||
* Most of high level scripts are written in perl | * Most of high level scripts are written in perl | ||
- | * Tested the program in small dataset and obtained contigs | + | * Runs from a shell script and a user-provided config file |
+ | * SGE-aware, handles qsub and monitoring jobs | ||
+ | * Pipeline is well sub-divided, running the program produces intermediate files and executables allowing the user to suspend, resume, or restart the run from any step in the pipeline | ||
+ | * Thorough error logging for each step in the algorithm | ||
+ | * Tested the program with the packaged test data and obtained contigs | ||
=====Installation===== | =====Installation===== | ||
- | * Main issue was get all dependencies together | + | * Main issue was new version of GCC and getting all the dependencies together ~16 hrs |
- | * There was one non-standard perl mode needed | + | * There was one non-standard perl module needed |
+ | * Files with carriage returns | ||
* Some scripts contain error but they aren't hard to fix. | * Some scripts contain error but they aren't hard to fix. | ||
=====Running Meraculous===== | =====Running Meraculous===== |