fix md5

ICGC-TCGA-PanCancer · Feb 14, 2018 · 61eb04c · 61eb04c
1 parent fc24497
commit 61eb04c
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Showing 2 changed files with 3 additions and 2 deletions.
diff --git a/workflow/tools/download.py b/workflow/tools/download.py
@@ -9,7 +9,7 @@
 task_dict = get_task_dict(sys.argv[1])
 cwd = os.getcwd()
 
-time.sleep(2*60)
+#time.sleep(2*60)
 
 def download_file(object_id, out_dir, file_name):
     docker_container = "quay.io/baminou/minibam-collab-dckr:latest"

diff --git a/workflow/tools/generate_song_payloads.py b/workflow/tools/generate_song_payloads.py
@@ -29,7 +29,8 @@ def create_payload_json(bam, analysis, experiment, input_directory, output_file)
     experiment_payload = ExperimentPayload(aligned=experiment.get('aligned'),library_strategy=experiment.get('library_strategy'),reference_genome=experiment.get('reference_genome'))
 
     file_path = os.path.join(input_directory,bam.get('minibam').get('bam_file_name'))
-    minibam_payload = FilePayload(file_access=bam.get('minibam').get('access'),file_name=bam.get('minibam').get('bam_file_name'),md5sum=hashlib.md5(file_path),file_type='BAM',file_size=os.stat(file_path).st_size)
+    minibam_payload = FilePayload(file_access=bam.get('minibam').get('access'),file_name=bam.get('minibam').get('bam_file_name'),
+                                  md5sum=hashlib.md5(open("nohup3.1.log",'rb').read()).hexdigest(),file_type='BAM',file_size=os.stat(file_path).st_size)
 
     file_path = os.path.join(input_directory,normal_bam.get('minibam').get('bai_file_name'))
     minibai_payload = FilePayload(file_access=normal_bam.get('minibam').get('access'),file_name=normal_bam.get('minibam').get('bai_file_name'),md5sum=hashlib.md5(file_path),file_type='BAI',file_size=os.stat(file_path).st_size)