Rename dldp/dldp/heatmap_pred/heatmap_main.sh to dldp/dldp/heatmap_pred/HPC_SC20/heatmap_main.sh

heatmap_main.sh

@@ -0,0 +1,44 @@
+#$ -cwd
+#$ -A  weizhe.li
+#$ -l h_rt=001:00:00
+#$ -S /bin/sh
+#$ -j y
+#$ -o sysout_heatmap
+#$ -N heatmap_main
+
+echo "Running job $JOB_ID on $HOSTNAME"
+
+QSUB=/opt/sge_root/bin/lx-amd64/qsub
+ARRAY_SCRIPT=heatmap_ar.sh
+
+declare -A dimensions
+dimensions[normal]="/home/weizhe.li/li-code4hpc/pred_dim_0314/training-updated/normal/dimensions"
+dimensions[tumor]="/home/weizhe.li/li-code4hpc/pred_dim_0314/training-updated/tumor/dimensions"
+dimensions[test]="/home/weizhe.li/li-code4hpc/pred_dim_0314/testing/dimensions"
+
+declare -A index_paths
+index_paths[normal]="/home/weizhe.li/li-code4hpc/pred_dim_0314/training-updated/normal/patch_index"
+index_paths[tumor]="/home/weizhe.li/li-code4hpc/pred_dim_0314/training-updated/tumor/patch_index"
+index_paths[test]="/home/weizhe.li/li-code4hpc/pred_dim_0314/testing/patch_index"
+
+slide_category=$1       # expects normal, tumor or test
+Folder_dimension=${dimensions[$slide_category]}
+slide_path=${slide_paths[$slide_category]}
+index_path=${index_paths[$slide_category]}
+
+Folder_Prediction_Results=$2
+# expect like this: "/scratch/mikem/UserSupport/weizhe.li/runs_process_cn_True/normal_wnorm_448_400_7690666"
+
+listfile="$slide_category"_preds_list     
+ls -1 "$Folder_Prediction_Results" | grep $slide_category > $listfile
+
+num=`ls -1 "$Folder_Prediction_Results" | grep $slide_category | wc -l`
+
+SYSOUT_DIR="$Folder_Prediction_Results"/heatmap_sysout
+mkdir -p $SYSOUT_DIR 
+
+# test
+# num=2
+
+ARRAY_SCRIPT=heatmap_arr.sh
+$QSUB -pe thread 1 -t 1-"$num" -o $SYSOUT_DIR  $ARRAY_SCRIPT  $listfile $Folder_Prediction_Results $Folder_dimension $index_path