Update get-version : #90

popen a shell command with module load before the porechop command

workflows/ont_qc/components/trimporechop.py

@@ -124,10 +124,12 @@ class Trim_porechop (Analysis):
         logging.getLogger("jflow").debug("End Trimporechop.post_process! ")
     
     def get_version(self):
-        #os.system("module load bioinfo/Porechop-0.2.1")
-        cmd = [self.get_exec_path("porechop"), "--version"]
+        shell_script = "module load compiler/gcc-7.2.0;module load bioinfo/Porechop-0.2.1;" + self.get_exec_path("porechop") + " --version"
+        logging.getLogger("jflow").debug("Trimporechop.get_version ! shell_script " + str(shell_script))
+        cmd = ["sh","-c",shell_script]
         p = Popen(cmd, stdout=PIPE, stderr=PIPE)
         stdout, stderr = p.communicate()
+        logging.getLogger("jflow").debug("Trimporechop.get_version !" + str(stderr))
         return stdout
                      
     def process(self):