Merge remote-tracking branch 'origin/feature/#46-luigi-integration-br…

…ian' into feature/#46-luigi-integration-brian

README.md

@@ -205,6 +205,9 @@ This script runs an unlimited number of BAM file uploads at random intervals.  T
     cd luigi_task_executor
     python simulate_analysis.py --es-index-host localhost --es-index-port 9200 --ucsc-storage-client-path ../ucsc-storage2-client --ucsc-storage-host https://storage2.ucsc-cgl.org
 
+    # temp
+    git hf update; git hf pull; PYTHONPATH='' luigi --module AlignmentQCTask AlignmentQCCoordinator --es-index-host localhost --es-index-port 9200 --ucsc-storage-client-path ../ucsc-storage2-client --ucsc-storage-host https://storage2.ucsc-cgl.org --tmp-dir `pwd`/luigi_state --data-dir /mnt/AlignmentQCTask --max-jobs 1
+
 ### populate dashboard
 
     cd Dashboard

luigi_task_executor/simulate_analysis.py

@@ -5,6 +5,7 @@
 import random
 
 # TODO: need to paramerterize the bam file used
+# TODO: some hardcoded paths below
 
 def getOptions():
 
@@ -25,7 +26,7 @@ def main():
         upload_count += 1
         print "LOOP ANALYSIS: "+str(upload_count)
 
-        cmd = "mkdir -p <HERE> && PYTHONPATH='' luigi --module AlignmentQCTask AlignmentQCCoordinator --es-index-host %s --es-index-port %s --ucsc-storage-client-path %s --ucsc-storage-host %s" % (args.es_index_host, args.es_index_port, args.ucsc_storage_client_path, args.ucsc_storage_host)
+        cmd = "mkdir -p /mnt/AlignmentQCTask && PYTHONPATH='' luigi --module AlignmentQCTask AlignmentQCCoordinator --es-index-host %s --es-index-port %s --ucsc-storage-client-path %s --ucsc-storage-host %s --tmp-dir `pwd`/luigi_state --data-dir /mnt/AlignmentQCTask --max-jobs 1" % (args.es_index_host, args.es_index_port, args.ucsc_storage_client_path, args.ucsc_storage_host)
         print "CMD: %s" % cmd
         result = subprocess.call(cmd, shell=True)
         if (result != 0):