User Tools

Site Tools


lecture_notes:04-20-2015

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revision Previous revision
Next revision
Previous revision
Last revision Both sides next revision
lecture_notes:04-20-2015 [2015/04/24 20:01]
calef [Installation]
lecture_notes:04-20-2015 [2015/04/24 20:06]
calef [Running Meraculous]
Line 22: Line 22:
   * 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+  * Tested the program ​with the packaged test data and obtained contigs
 =====Installation===== =====Installation=====
   * Main issue was new version of GCC and getting all the dependencies together ~16 hrs    * Main issue was new version of GCC and getting all the dependencies together ~16 hrs 
Line 29: Line 29:
   * 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