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@@ -1,8 +1,8 @@
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[1 Image patch extraction](#1-image-patch-extraction)
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-[1.3 Retreiving wall-clock time statistics for extraction and grouping](#1.3-Retreiving-wall-clock-time-statistics-for-extraction-and-grouping)
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[2 Prediction](#2-prediction)
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[3 Heatmap stitching](#3-heatmap-stitching)
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[4 Retreiving run-time statistics for prediction](#4-Retreiving-run-time-statistics-for-prediction)
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+[5 Retreiving wall-clock time statistics for extraction and grouping](#5-Retreiving-wall-clock-time-statistics-for-extraction-and-grouping)
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# 1 Image patch extraction
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@@ -21,13 +21,6 @@
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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.
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-## 1.3 Retreiving wall-clock time statistics for extraction and grouping
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-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:
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-- time bash time_stats_sg_V2.sh [test | normal | tumor] ROOT_DIR
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-
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-An example run:
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-- time bash wall_clock_time_split_group_V2.sh test /scratch/mikem/UserSupport/weizhe.li/runs_split_group/448_400_7691440
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-
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# 2 Prediction
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- Additionally adjust configuration parameters in files, *config_testing_cn_true.txt*, *config_normal_cn_true.txt*, *config_tumor_cn_true.txt*.
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- Run commands listed in the below subsections to launch SGE jobs to generate prediction matrices.
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@@ -60,4 +53,10 @@ In *wall_clock_time_stats_pred.sh* file adjust job results root directory, DIR a
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Then run:
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- time bash ./wall_clock_time_stats_pred.sh
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+# 5 Retreiving wall-clock time statistics for extraction and grouping
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+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:
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+- time bash time_stats_sg_V2.sh [test | normal | tumor] ROOT_DIR
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+
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+An example run:
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+- time bash wall_clock_time_split_group_V2.sh test /scratch/mikem/UserSupport/weizhe.li/runs_split_group/448_400_7691440
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