|
@@ -43,18 +43,18 @@ The \*.sh files mentioned in sections 2.1 and 2.2 below are located under <a hr
|
|
|
|
|
|
|
|
# 3 Heatmap stitching
|
|
# 3 Heatmap stitching
|
|
|
After the predictions matrices have been generated an SGE job using *heatmap_main.sh* SGE scrip could be launched to genertae heatmaps. Two arguments for this launch are: a) type of the slides (test, normal or tumor); b) the root directory of the results, like in below example run:
|
|
After the predictions matrices have been generated an SGE job using *heatmap_main.sh* SGE scrip could be launched to genertae heatmaps. Two arguments for this launch are: a) type of the slides (test, normal or tumor); b) the root directory of the results, like in below example run:
|
|
|
-- qsub heatmap_main.sh test /scratch/mikem/UserSupport/weizhe.li/runs_process_cn_True/testing_wnorm_448_400_7690953
|
|
|
|
|
|
|
+- qsub heatmap_main.sh test results_directory
|
|
|
-- *heatmap_main.sh* in turn calls *heatmap_arr.sh* which runs *heatmap_assembly.py* for the heatmap stitching of all slides in parallel/scalable manner.
|
|
-- *heatmap_main.sh* in turn calls *heatmap_arr.sh* which runs *heatmap_assembly.py* for the heatmap stitching of all slides in parallel/scalable manner.
|
|
|
# 4 Retreiving run-time statistics for prediction
|
|
# 4 Retreiving run-time statistics for prediction
|
|
|
## 4.1 CPU time
|
|
## 4.1 CPU time
|
|
|
In *time_all_stats_pred.sh* file adjust job results root directory, DIR and slides type, PREFIX (normal, test or tumor), like below:
|
|
In *time_all_stats_pred.sh* file adjust job results root directory, DIR and slides type, PREFIX (normal, test or tumor), like below:
|
|
|
-- DIR=/scratch/mikem/UserSupport/weizhe.li/runs_process_cn_False/normal_wnorm_448_400_7691563
|
|
|
|
|
|
|
+- DIR=results_directory
|
|
|
- PREFIX=normal
|
|
- PREFIX=normal
|
|
|
Then run:
|
|
Then run:
|
|
|
- time bash ./time_all_stats_pred.sh
|
|
- time bash ./time_all_stats_pred.sh
|
|
|
## 4.2 Wall-Clock time
|
|
## 4.2 Wall-Clock time
|
|
|
In *wall_clock_time_stats_pred.sh* file adjust job results root directory, DIR and slides type, PREFIX (normal, test or tumor), like below:
|
|
In *wall_clock_time_stats_pred.sh* file adjust job results root directory, DIR and slides type, PREFIX (normal, test or tumor), like below:
|
|
|
-- DIR=/scratch/mikem/UserSupport/weizhe.li/runs_process_cn_V2_False/testing_wnorm_448_400_7694088
|
|
|
|
|
|
|
+- DIR=results_directory
|
|
|
- PREFIX=test
|
|
- PREFIX=test
|
|
|
Then run:
|
|
Then run:
|
|
|
- time bash ./wall_clock_time_stats_pred.sh
|
|
- time bash ./wall_clock_time_stats_pred.sh
|
Mike Mikailov