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Mike Mikailov 5 年之前
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      readme.md

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readme.md

@@ -1,8 +1,8 @@
 [1 Image patch extraction](#1-image-patch-extraction)  
 [1 Image patch extraction](#1-image-patch-extraction)  
-[1.3 Retreiving wall-clock time statistics for extraction and grouping](#1.3-Retreiving-wall-clock-time-statistics-for-extraction-and-grouping)  
 [2 Prediction](#2-prediction)  
 [2 Prediction](#2-prediction)  
 [3 Heatmap stitching](#3-heatmap-stitching)  
 [3 Heatmap stitching](#3-heatmap-stitching)  
 [4 Retreiving run-time statistics for prediction](#4-Retreiving-run-time-statistics-for-prediction)  
 [4 Retreiving run-time statistics for prediction](#4-Retreiving-run-time-statistics-for-prediction)  
+[5 Retreiving wall-clock time statistics for extraction and grouping](#5-Retreiving-wall-clock-time-statistics-for-extraction-and-grouping)  
 
 
 
 
 # 1 Image patch extraction
 # 1 Image patch extraction
@@ -21,13 +21,6 @@
 
 
 The lookup tables are created only once and used at [Prediction](#2-prediction) stage for launching array job tasks. These tasks are run in parallel and scalable manner - if there are not enough resourcs for running all tasks then they are queued up automatically and started as resources become available. Each task processes only one group. 
 The lookup tables are created only once and used at [Prediction](#2-prediction) stage for launching array job tasks. These tasks are run in parallel and scalable manner - if there are not enough resourcs for running all tasks then they are queued up automatically and started as resources become available. Each task processes only one group. 
 
 
-## 1.3 Retreiving wall-clock time statistics for extraction and grouping
-Run *time_stats_sg_V2.sh* Linux scrip with two arguments: a) type of slides (test, normal or tumor) and b) the root directory of the results:
-- time bash time_stats_sg_V2.sh [test | normal | tumor] ROOT_DIR  
-
-An example run:  
-- time bash wall_clock_time_split_group_V2.sh test /scratch/mikem/UserSupport/weizhe.li/runs_split_group/448_400_7691440  
-
 # 2 Prediction
 # 2 Prediction
 - Additionally adjust configuration parameters in files, *config_testing_cn_true.txt*, *config_normal_cn_true.txt*, *config_tumor_cn_true.txt*.
 - Additionally adjust configuration parameters in files, *config_testing_cn_true.txt*, *config_normal_cn_true.txt*, *config_tumor_cn_true.txt*.
 - Run commands listed in the below subsections to launch SGE jobs to generate prediction matrices.
 - Run commands listed in the below subsections to launch SGE jobs to generate prediction matrices.
@@ -60,4 +53,10 @@ In *wall_clock_time_stats_pred.sh* file adjust job results root directory, DIR a
 Then run:  
 Then run:  
 - time bash ./wall_clock_time_stats_pred.sh  
 - time bash ./wall_clock_time_stats_pred.sh  
 
 
+# 5 Retreiving wall-clock time statistics for extraction and grouping
+Run *time_stats_sg_V2.sh* Linux scrip with two arguments: a) type of slides (test, normal or tumor) and b) the root directory of the results:
+- time bash time_stats_sg_V2.sh [test | normal | tumor] ROOT_DIR  
+
+An example run:  
+- time bash wall_clock_time_split_group_V2.sh test /scratch/mikem/UserSupport/weizhe.li/runs_split_group/448_400_7691440