Add ###USER### placeholder in storage section.

application.properties

@@ -47,6 +47,7 @@ from_password =
 #message =
 
 [storage]
+# In this section, ###USER### (if it's used) is replaced by $USER environment variable.
 # where should be written the log file
 log_file = <path>/jflow.log
 # Where should the pipelines write results, should be accessible 

docs/jflow_advanced_configuration.html

@@ -219,8 +219,13 @@
         	<section id="storage" class="group">
 		    	<h1 class="page-header">Storage <small>section</small></h1>
 		    	<p>
-		    		This section configure the paths used by all workflows. 
+		    		This section configure the paths used by all workflows.
 		    	</p>
+		    	<p>
+		    		On a multi-user computer or cluster you can use placeholder <code>###USER###</code>.
+		    		<code>###USER###</code> will be replace by the environment variable <code>$USER</code>.
+		    	</p>
+		    	
 		    	<div class="table-responsive">
 					<table class="table table-bordered table-striped">
 						<thead>

src/jflow/config_reader.py

@@ -37,12 +37,12 @@ class JFlowConfigReader(object):
         self.reader.read(os.path.join(os.path.dirname(inspect.getfile(self.__class__)), self.CONFIG_FILE_PATH))
 
     def get_tmp_directory(self):
-        if not os.path.isdir(self.reader.get("storage", "tmp_directory")):
-            os.makedirs(self.reader.get("storage", "tmp_directory"), 0o751)
-        return self.reader.get("storage", "tmp_directory")
+        if not os.path.isdir(self.reader.get("storage", "tmp_directory").replace("###USER###",os.getenv("USER"))):
+            os.makedirs(self.reader.get("storage", "tmp_directory").replace("###USER###",os.getenv("USER")), 0o751)
+        return self.reader.get("storage", "tmp_directory").replace("###USER###",os.getenv("USER"))
         
     def get_work_directory(self):
-        return self.reader.get("storage", "work_directory")
+        return self.reader.get("storage", "work_directory").replace("###USER###",os.getenv("USER"))
     
     def get_exec(self, software):
         try:
@@ -59,7 +59,7 @@ class JFlowConfigReader(object):
           @return: the path to the log file
         """
         try:
-            return self.reader.get('storage', 'log_file')
+            return self.reader.get('storage', 'log_file').replace("###USER###",os.getenv("USER"))
         except :
             raise NoOptionError("Failed when parsing the config file, no section logging found!")