|
@@ -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
|
|
|
|
|
|
Mike Mikailov