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lecture_notes:04-20-2015

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lecture_notes:04-20-2015 [2015/04/24 20:03]
calef [User experience]
lecture_notes:04-20-2015 [2015/04/24 20:06]
calef [Running Meraculous]
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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
-  * 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   * Tested the program with the packaged test data and obtained contigs
 =====Installation===== =====Installation=====
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   * 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=====
-  * Execute run_meraculous.sh scripts along with the configuration file+  * Execute run_meraculous.sh scripts along with user-provided ​configuration file
   * Configuration file contains info on where where data is and what format it comes in   * Configuration file contains info on where where data is and what format it comes in
-  * It creates ​a timestamped folder that includes directories containing results of each step and executables to modify ​the run +  * Creates ​a timestamped folder that includes directories containing results of each step and executables to suspend, resume, or restart ​the run from that step 
-  * Then you can check the errors that made a run fail and resume the run +  * Thorough error-logging at each step, allowing ​you to check the errors that made a run fail and then resume the run after fixing the errors 
-  * Logs are informative+  * SGE-aware, handles qsub and monitoring jobs
 =====Overall impression===== =====Overall impression=====
   * Straightforward to figure out what went wrong just requiring a basic understanding of Perl   * Straightforward to figure out what went wrong just requiring a basic understanding of Perl
lecture_notes/04-20-2015.txt · Last modified: 2015/04/24 20:07 by calef