better logging to s3 clone

Daylily-Informatics · Dec 2, 2024 · c14160b · c14160b
1 parent 9599411
commit c14160b
Showing 1 changed file with 11 additions and 11 deletions.
diff --git a/bin/create_daylily_omics_analysis_s3.sh b/bin/create_daylily_omics_analysis_s3.sh
@@ -222,30 +222,30 @@ else
     echo "Running the following commands serially"
 
     echo ""
-    echo "NOW RUNNING"
+    echo "NOW RUNNING 1 of 11"
     echo "...$cmd_version"
     $cmd_version >> $LOGFILE 2>&1  && echo "success" || echo ">>>FAILED<<< will be fatal" && overall_status='FAILED'
 
     echo " "
-    echo "NOW RUNNING"
+    echo "NOW RUNNING 2 of 11"
     echo "...$cmd_cluster_boot_config"
     $cmd_cluster_boot_config  >> $LOGFILE 2>&1 && echo "success" || echo ">>>FAILED<<< will be fatal" && overall_status='FAILED'
 
 
-    echo "NOW RUNNING"
+    echo "NOW RUNNING 3 of 11"
     echo "... $cmd_cached_envs"
     $cmd_cached_envs >> $LOGFILE 2>&1 && echo "success" || echo ">>>FAILED<<< prob ok, but unexpected" && overall_status='FAILED'
 
-    echo "NOW RUNNING"
+    echo "NOW RUNNING 4 of 11"
     echo "...$cmd_libs"
     $cmd_libs >> $LOGFILE 2>&1  && echo "success" || echo ">>>FAILED<<< will be fatal" && overall_status='FAILED'
 
 
-    echo "NOW RUNNING"
+    echo "NOW RUNNING 5 of 11"
     echo "...$cmd_tool_specific_resources"
     $cmd_tool_specific_resources  >> $LOGFILE 2>&1  && echo "success" || echo ">>>FAILED<<< will be fatal" && overall_status='FAILED'
 
-    echo "NOW RUNNING"
+    echo "NOW RUNNING 6 of 11"
     echo "...$cmd_budget"
     $cmd_budget  >> $LOGFILE 2>&1  && echo "success" || echo ">>>FAILED<<< will be fatal" && overall_status='FAILED'
 
@@ -256,11 +256,11 @@ else
         echo "$cmd_hg38_ref"
         echo "$cmd_hg38_annotations"
     else
-        echo "NOW RUNNING"
+        echo "NOW RUNNING 7 of 11"
         echo "...$cmd_hg38_ref"
         $cmd_hg38_ref  >> $LOGFILE 2>&1  && echo "success" || echo ">>>FAILED<<< will be fatal if hg38 is needed" && overall_status='FAILED'
 
-        echo "NOW RUNNING"
+        echo "NOW RUNNING 8 of 11"
         echo "...$cmd_hg38_annotations"
         $cmd_hg38_annotations >> $LOGFILE 2>&1  && echo "success" || echo ">>>FAILED<<< will be fatal if hg38 is needed" && overall_status='FAILED'
 
@@ -271,11 +271,11 @@ else
         echo "$cmd_b37_ref"
         echo "$cmd_b37_annotations"
     else
-        echo "NOW RUNNING"
+        echo "NOW RUNNING 9 of 11"
         echo "...$cmd_b37_ref"
         $cmd_b37_ref  >> $LOGFILE 2>&1   && echo "success" || echo ">>>FAILED<<< will be fatal if b37 is needed" && overall_status='FAILED'
 
-        echo "NOW RUNNING"
+        echo "NOW RUNNING 10 of 11"
         echo "...$cmd_b37_annotations"
         $cmd_b37_annotations >> $LOGFILE 2>&1 && echo "success" || echo ">>>FAILED<<< will be fatal if b37 is needed" && overall_status='FAILED'
 
@@ -285,7 +285,7 @@ else
         echo "Skipping GIAB reads copy:"
         echo "$cmd_giab_reads"
     else
-        echo "NOW RUNNING"
+        echo "NOW RUNNING 11 of 11"
         echo "...$cmd_giab_reads"
         $cmd_giab_reads >> $LOGFILE 2>&1 && echo "success" || echo ">>>FAILED<<< will be fatal if GIAB reads are needed" && overall_status='FAILED'