send_json_data.sh

added the send_json_data bash script to post cellranger GEX and VDJ data to RUN QC.  the /home/igo/Scripts where the script was previously stored was deleted, therefore causing an error when trying to post GEX and VDJ data to RUN QC

scripts/cellranger.py

@@ -191,7 +191,7 @@ def create_json(send_json, sequencer_and_run, project, tag, work_area):
     with open(json_data_file, "w") as jfile:
         json.dump(send_json, jfile)
 
-    bsub_json = "bsub -J create_json___{} -o create_json___{}.log -w \"done({}*)\" sh /home/igo/Scripts/PicardScripts/send_json_data.sh {} {}".format(job_id, job_id, job_id, work_area, json_data_file)
+    bsub_json = "bsub -J create_json___{} -o create_json___{}.log -w \"done({}*)\" sh /igo/work/igo/igo-demux/scripts/send_json_data.sh {} {}".format(job_id, job_id, job_id, work_area, json_data_file)
     print(bsub_json)
     subprocess.run(bsub_json, shell = True)
 

scripts/send_json_data.sh

@@ -0,0 +1,18 @@
+#!/bin/bash
+
+
+##Usage sh send_json_data.sh patth_to_json json_file  
+args=$@
+
+path_to_json=$1
+json_file=$2
+
+cd $path_to_json
+
+echo $path_to_json
+json_data=$(cat $json_file)
+echo $json_data
+
+
+curl -d "$json_data" -H "Content-Type: application/json" -X POST "http://igodb.mskcc.org:8080/ngs-stats/saveCellRangerSample"
+